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Archive for the ‘Personalized and Precision Medicine & Genomic Research’ Category

Reporter: Aviva Lev-Ari, PhD, RN

Countries colored in brown rank highly in the Growth Competitiveness Index 2004 – 2005, World Economic Forum. Black circles represent select biotechnology and life sciences clusters.

North AmericaSeattle, USA
San Francisco, USA
Los Angeles, USA
San Diego, USA
Saskatoon, Canada
*Minneapolis/St. Paul/Rochester USA
Austin, USA
Toronto, Canada
Montreal, Canada
Boston, USA
New York/New Jersey, USA
Philadelphia, USA
Baltimore/Washington, DC, USA
Research Triangle NC, USA
Central America / South AmericaWest Havana, Cuba
Belo Horizonte/Rio de Janeiro, Brazil
Sao Paulo, Brazil
United Kingdom / IrelandGlasgow-Edinburgh, Scotland
Manchester-Liverpool, England
London, England
Cambridge-SE England
Dublin, Republic of Ireland
Continental EuropeBrussels, Belgium
Medicon Valley, Denmark/Sweden
Stockholm/Uppsala, Sweden
Helsinki, Finland
Paris, France
Biovalley, France/Germany/Switzerland
BioAlps, France/Switzerland
Sophia-Antipolis, France
BioRhine, Germany
BioTech Munich, Germany
BioCon Valley, Germany
MideastIsrael AfricaCapetown,
South Africa
AsiaBeijing, China
Shanghai, China
Shenzhen, China
Hong Kong, China
Tokyo-Kanto, Japan
Kansai, Japan
Hokkaido, Japan
Taipei, Taiwan
Hsinchu, Taiwan
Singapore
Dengkil, Malaysia
New Delhi, India
Hyderabad, India
Bangalore, India
OceaniaBrisbane, Australia
Sydney, Australia
Melbourne, Australia
Dunedin, New Zealand

Definitions

Biotechnology: Biotechnology is the use of cellular and biomolecular processes to solve problems or make useful products. [Biotechnology Industry Organization – BIO]

Bioscience/Life Science: pharmaceuticals, biotechnology, medical devices, R&D in the life sciences. [Devol et al., 2005]

Clusters: Clusters are a geographically proximate group of interconnected companies and associated institutions in a particular field, including product producers, service providers, suppliers, universities, and trade associations. [Cluster Mapping Project, Institute for Strategy and Competitiveness, Harvard Business School]

* Cited no. 8 for Total Life Sciences Current Impact by Devol (2005) defined as pharmaceutical, biotechnology, medical devices, and R&D in the life sciences. Minneapolis/St. Paul/Rochester is principally a medical device cluster.

References

Map is a Mercator projection that exaggerates the size of areas far from the equator.

Global biotechnology clusters map published by:

Andersen, Jørn Bang, “Establishment of Nordic Innovation Centres in Asia?” by the Nordic Innovation Centre for the Nordic Council of Ministers, Copenhagen, 2008.

Dimova, Maria, Andres Mitnik, Paula Suarez-Buitron and Marcos Siqueira. “Brazil Biotech Cluster: Minas Gerais” [PDF] Institute for Strategy and Competitiveness, Harvard Business School, Spring 2009.

Encyclopedia of Globalization, Routledge, November 2006.

Hamdouch, Abdelillah and Feng He. “R&D Offshoring and Clustering Dynamics in Pharmaceuticals and Biotechnology: Insights from the Chinese Case,” [PDF] The Spirit of Innovation Forum III, May 14-16, 2007.

Loh, Melvyn Wei Ming, “Riding the Biotechnology Wave: A Mixed-Methods Analysis of Malaysia’s emerging Biotechnology industry” [PDF] Victoria University of Wellington, New Zealand, 2009.

Murray, Fiona and Helen Hsi, “Knowledge Workers in Biotechnology: Occupational Structures, Careers & Skill Demands” [PDF] MIT Sloan School of Management, September 2007.

Rinaldi, Andrea. “More than the sum of their parts? Clustering is becoming more prevalent in the biosciences, despite concerns over the sustainability and economic effectiveness of science parks and hubs,”EMBO reports, February 2006 [PDF]

Royer, Susanne, “Crossing-borders: International Clusters: An analysis of Medicon Valley based on Value-Adding Web “ [PDF] University of Flensburg, July 8, 2007.

Salerno, Reynolds. “International Biological Threat Reduction at Sandia,” Sandia National Laboratory, July 31, 2006 [PDF]

Source:

http://biotech.about.com/gi/o.htm?zi=1/XJ&zTi=1&sdn=biotech&cdn=b2b&tm=7&f=00&tt=3&bt=1&bts=1&zu=http%3A//mbbnet.umn.edu/scmap/biotechmap.html

The 26th annual issue of Beyond borders, E&Y annual report on the global biotechnology industry.

Our analysis of trends across the leading centers of biotech activity reveals both signs of hope and causes for concern. The financial performance of publicly traded companies is more robust than at any time since the onset of the global financial crisis, with the industry returning to double-digit revenue growth.

Companies that had made drastic cuts in R&D spending in the aftermath of the crisis are now making substantial increases in their pipeline development efforts.

But even as things are heading back to normal on the financial performance front, the financing situation remains mired in the “new normal” we have been describing for the last few years. While the biotech industry raised more capital in 2011 than at any time since the genomics bubble of 2000, this increase was driven entirely by large debt financings by the industry’s commercial leaders.

The money flowing to the vast majority of smaller firms, including pre-commercial, R&D-phase companies — a measure we refer to as “innovation capital” — has remained flat for the last several years.

As such, the question we have posed for the last two years is more relevant than ever: how can biotech innovation be sustained during a time of serious resource constraints?

These are timely topics, and we look forward to exploring them with you.

Take a closer look at our findings and point of view:

  • Holistic open learning networks -Holistic open learning networks (HOLNets) could make R&D shades more efficient by harnessing the power of big data to develop real-time insights.Even as biotech adjusts to its new normal, health care is moving to an outcomes-based ecosystem characterized by new incentives, new technologies and big data.

    HOLNets could reinvent R&D by pooling data, creating standards and engaging regulators and patients.

    Now, more than ever, this approach is feasible because it is in the self interest of the entities that would need to be part of it.

  • Financial performance heads back to normal -The aggregate financial performance of publicly traded biotechnology companies in the four established clusters — the United States, Europe, Canada and Australia — showed encouraging signs of recovery and stabilization.Growth in established biotechnology centers, 2010-11 (US$b)

    Source: Ernst & Young and company financial statement data.
    Numbers may appear inconsistent because of rounding.

    The acquisition of three large US companies — Genzyme Corp., Cephalon and Talecris Biotherapeutics —by non-biotech buyers made a significant dent in the industry’s 2011 performance.

    To get a sense of the organic “apples-to-apples” growth of the industry, we have therefore calculated normalized growth rates that remove these three firms from the 2010 numbers.

    After adjusting for these large acquisitions, the industry’s revenue growth rate returned to double-digit territory for the first time since the global financial crisis. R&D grew by 9% in 2011, after being slashed in 2009 and growing by a modest 2% in 2010.

    US biotechnology at a glance, 2010-11 (US$b)

    Source: Ernst & Young and company financial statement data.
    Numbers may appear inconsistent because of rounding.

    As always, since the US accounts for a large majority of the industry’s revenues, the US story is very similar to the global one.

    After normalizing for the acquisitions of Genzyme, Cephalon and Talecris , the US industry’s revenues increased by 12%, outpacing the 10% growth rate seen in 2010 and 2009 (adjusted for the Genentech acquisition).

    Source:

    http://www.ey.com/GL/en/Industries/Life-Sciences/Beyond-borders—global-biotechnology-report-2012_Financial-performance-heads-back-to-normal


  • Financing remains stuck in the “new normal”
  • Big pharma stayed away from M&A deals -Given the critical role that big pharma could play in supporting the biotech innovation ecosystem and the fact that the expected exit for most venture investors is an acquisition, this lack of activity is unsettling.With big pharma in the midst of crossing the long-awaited patent cliff, many expected a more pronounced upsurge in transactions — particularly for targets with product revenue or very late-stage product candidates.

    However, only Sanofi’s acquisition of Genzyme (which really played out in 2010 but did not get finally negotiated and closed until 2011) entered the ranks of the year’s 10 largest deals. Even more noteworthy, big pharma was the buyer in only 7 of the year’s 57 M&A transactions.

    US and European M&As, 2006-11

    US and European M&As, 2006-11Source: Ernst & Young, Capital IQ, MedTRACK and company news.
    Chart excludes transactions where deal terms were not publicly disclosed.

    Meanwhile, the number of strategic alliances declined for the second straight year, and the potential “biobucks” value of these deals hit a six-year low.

    US and European strategic alliances based on up-front payments, 2006-11

    US and European strategic alliances based on up-front payments, 2006-11



Source:

http://www.ey.com/GL/en/Industries/Life-Sciences/Beyond-borders—global-biotechnology-report-2012-Big-pharma-stayed-away-from-MandA-deals

http://www.ey.com/GL/en/Industries/Life-Sciences/Beyond-borders—global-biotechnology-report-2012

Resizing the Global Contract R&D Services Market

 A new study revises estimates of the market

By Kenneth Getz, Mary Jo Lamberti, Adam Mathias, Stella Stergiopoulos, Tufts CSDD

Published May 30, 2012

Pharmaceutical, biotechnology and medical device company managers serving every R&D function — from discovery and manufacturing through post-approval clinical trials — are keenly aware today of the integral role that outsourcing plays in supplementing capacity and expertise. Demand for outsourced services has increased sharply as drug and device development sponsors have downsized and consolidated infrastructure in response to a sharp global economic downturn, poor short-term revenue growth prospects and costly and inefficient operating conditions. In addition, startups and small companies actively leverage contract service providers to gain access to expertise and skills not available internally.Contract service organizations have proliferated across a wide spectrum of R&D services areas. A 2011 analysis by Tufts Center for the Study of Drug Development (Tufts CSDD) found a nearly four-fold increase in the number of contract research organizations (CROs) in the U.S. alone during the past decade: Whereas an estimated 800 contract service providers operated in the U.S. in 2000, more than 3,100 did so at the end of 2011. (Data on the proliferation of contract R&D service providers in Europe and in other regions around the world are not available.) In another study, Tufts CSDD found that in 2010, CRO-employed professionals were more than doubling the capacity of the global drug development enterprise — the first time in history when CROs were providing more head count in support of R&D activity than were pharma and biopharma companies.

Despite this dramatic proliferation during the last 10 years, however, little information exists that characterizes the size and characteristics of the overall global outsourcing landscape. Coverage of CRO markets and usage practices by peer-review and trade journals has largely focused on individual service areas aligned with either each publisher’s readership or the author’s primary area of expertise. Contract lead identification and optimization services markets and practices, for example, tend to be covered in publications reaching discovery scientists. Similarly, the contract formulation services area is typically discussed in publications catering to professionals in chemistry, manufacturing and controls. Some directories (e.g., Contract Pharma (www.contractpharma.com/csd), PharmaCircle (www.pharmacircle.com)) profile companies across contract R&D service areas. These directories do not publish macro-analyses of the global aggregate R&D outsourcing market.

Capital market analysts and industry observers have also largely focused on characterizing only the most mature R&D outsourcing markets: contract clinical and preclinical research services. These markets have historically had the highest prevalence of large, publicly-traded companies making it relatively easy to monitor performance, assess transactions and evaluate corporate strategies. Goldman Sachs, UBS, Fairmount Partners, Jefferies and William Blair are among the many financial services firms that support transactions and cover developments in the global outsourcing marketplace. Published reports from these organizations typically only cover and estimate the size of the clinical and preclinical markets — a fraction of the total contract services marketplace. Industry professionals and analysts tend to use these estimates as proxy measures for total market size when they grossly underestimate the size of the overall outsourcing market.

Two recent reports stand out as noteworthy attempts to size the overall CRO market and affirm the growing interest in this aggregate market metric: the Harris Williams & Company 2008 Market Monitor report and the 2011 BCC Research Report. The former report focused on the larger healthcare and life sciences arena but estimated — using a top-down approach — the size of the contract clinical, preclinical, manufacturing, clinical laboratory and sales markets. Harris Williams, a private investment banking firm, estimated that the total market for these specific service areas in 2008 reached approximately $75 billion. The later BCC Research report sized the overall 2011 global outsourcing market at $217.9 billion. This top-down analysis included not only contract service providers supporting prescription drugs, but also over-the-counter and nutraceuticals products.

As demand for — and the adoption of — contract research services has grown there is a greater need for more accurate and comprehensive measures of the size and structure of the overall landscape. Better metrics assist companies and analysts in assessing the financial health, trends, structure, operating conditions and maturity of the overall market for contract research services. Sponsor companies can also use these metrics for strategic planning purposes and to forecast the impact of new management practices on the landscape. More accurate metrics enable analysts to monitor consolidation, diversification and divestiture activities. And more accurate descriptive statistics on the landscape assist CRO companies in developing, implementing and evaluating strategic initiatives.

In late 2010, Tufts CSDD began a new study using a rigorous, bottom-up approach to independently size the U.S. market for all contract R&D services. The goal of the study was to perform a carefully designed, methodical and systematic market-sizing study using actual data wherever possible. It is our hope that this initial but definitive quantitative assessment will serve as a basis for sizing contract service providers in Europe and in the rest of the world, and that it will better inform discussion, analysis and understanding of the global outsourcing landscape.

Methods
Tufts CSDD focused on the U.S. market for this initial study due to the labor-intensive nature of analyzing a large, fragmented market predominantly made up of small, privately held organizations and independent consultants. Tufts CSDD developed detailed definitions of primary contract service markets, and compiled a list — to the best of its ability — of all known contract service providers in each respective market within high concentration metropolitan and industrial areas. A total of 15 major geographic clusters, defined by Metropolitan Statistical Area (MSA), were identified and analyzed. These clusters capture approximately 75% of the list of contract service companies operating in the US. Contract service companies operating within these 15 geographic regions likely capture an even larger proportion of total U.S. outsourced services revenue as these companies include all the major, widely-recognized players. Data on more than 4,500 companies — some of them divisions or branches of diversified players — were analyzed.

Market Segment Definitions: The five primary market segments evaluated correspond with primary R&D and manufacturing processes: Applied Research, Non-Clinical Research, Clinical Research, Chemistry Manufacturing and Controls (CMC) and Staffing-Consulting-Management (Other) services. This ‘Other’ segment includes a wide variety of small, independent companies as well as large providers offering contract professional staffing, supply chain management, import/ export and distribution services as well as business development support. Specific main service category and common sub-category service areas within each of the primary market segments are characterized in Figure 1. (Main Categories and Sub-Categories are not mutually exclusive.)

Figure 1: Service Area Map

Service Provider Identification: Tufts CSDD used seven published, commercially available print and online directories of contract service providers to identify individual contract R&D services companies:

  • Applied Clinical Trials 2010 Directory & Buyers Guide
  • Contract Pharma2010/2011 Contract Services Directory
  • Fierce Marketplace 2010/2011 Directory for Contract Manufacturing
  • Hoovers.com Biotechnology Services Directory
  • The Pharmaceutical OutsourcingTM 2011 Company Focus and Industry Reference Guide (Volume 11, Issue 6, October 2010)
  • The PharmaCircle Database 2010/2011
  • ReferenceUSA.com (SIC Code 591207; “Pharmaceutical Consultants”) as of December 2010

Top Areas of Geographic Concentration: From these directories, company names and addresses were captured. Each company’s main address zip code was organized according to the U.S. Office of Management and Budget (OMB)’s definition of Metropolitan Statistical Areas (MSA). This approach was used in order to systematically identify and analyze areas of highest geographic concentration. The OMB’s definition of the MSA is “one or more adjacent counties or county equivalents that have at least one urban core area of at least 50,000 population, plus adjacent territory that has a high degree of social and economic integration with the core as measured by commuting ties.” The largest 15 geographic areas, defined by MSAs, containing contract service providers are:

  • New York/Northern New Jersey (i.e., New York-Northern New Jersey-Long Island)
  • Greater Boston (i.e., Boston-Worcester-Lawrence)
  • Delaware Valley (i.e., Philadelphia-Wilmington-Atlantic City)
  • Los Angeles (i.e., Los Angeles-Riverside-Orange County)
  • The Washington DC Area
  • San Francisco Bay (i.e., San Francisco-Oakland-Freemont)
  • San Diego (i.e., San Diego-Carlsbad-San Marcos)
  • Durham NC (i.e., Durham-Chapel Hill)
  • Greater Chicago (i.e., Chicago-Joliet-Naperville)
  • Greater Baltimore (i.e., Baltimore-Towson)
  • Raleigh NC (i.e., Raleigh-Cary)
  • Minneapolis (i.e., Minneapolis-St. Paul-Bloomington)
  • Kansas City Area
  • San Jose (i.e., San Jose-Sunnyvale-Santa Clara)
  • Houston (i.e., Houston-Sugar Land-Baytown)

Figure 2 provides a visual representation of the 15 highest concentration areas of contract R&D services providers in the United States. These concentrated areas of contract service providers are in close proximity to geographic areas where pharmaceutical, biotechnology and manufacturing sectors in the US originated.

Figure 2: High Concentration Geographic Areas

Contract Service Company Types: Tufts CSDD organized companies along the following lines to assist with its evaluation of overall market and service segment characteristics:

  • Pure-play companies: companies offering only one service area main-category. Examples of pure-play companies include: Abpro Corporation, cGMP Validation LLC. and Profacgen.
  • Mid-sized companies: companies with two to five service area main-categories. Examples include: Accugenix Inc., Beckloff Associates Inc., QS Pharma and the Zitter Group.
  • Conglomerate companies: companies with six or more service areas main-categories. Examples include: Aptuit (multiple sites); Covance (multiple Sites); PPD (multiple sites) and Quest Diagnostics (multiple sites)

(Service areas are defined in Figure 1.)

Tufts CSDD used company websites to determine branch and satellite office locations. If a company did not have a website, it was removed from the analysis. If the website did not specify which site performed which service, it was assumed that all locations offered the same number of services.

For publicly traded companies, Tufts CSDD used published company reports — annual reports, 10Ks, trade journal and newspaper articles — for operating information, revenue figures, locations and employee size. For privately held companies, Tufts CSDD used Hoovers.com.

Actual revenues and employee data were used whenever possible. In those cases where actual data were not available, financial and employee data were imputed using benchmark metrics derived from actual data:

  • Pure-play companies: assigned average revenue and employee values based on actual data from other pure-play companies.
  • Mid-sized companies: derived revenue and employee values based on actual data from companies of equal size and diversity.
  • Conglomerate companies: derived revenue and employee values based on actual data from companies of equal size and diversity.
  • Public companies: If service area-specific revenue and employee data was not reported, values were distributed equally across service areas.

Results
In total, 3,244 unique contract R&D service companies actively operating in the U.S. were identified and analyzed. These companies generated an estimated $32.9 to $39.5 billion in contract R&D services revenue with the largest share coming from the CMC and Non-Clinical market segments — 29%, and 21% respectively. The U.S. Clinical Research Services segment — which includes regulatory services — generated approximately $6.5 billion. Chart 1 shows the relative U.S. market share of each contract R&D service segment.

In the aggregate, companies operating in the overall U.S. contract R&D services market employ approximately 154,000 people and were founded more than 17 years ago. The typical company is privately-held, generates $10 million ($US) in revenue annually and is operating in 1.4 service areas.

The CMC and Non-Clinical Research segments have the largest number of companies providing services as shown in Chart 2. An estimated 1,274 companies in the U.S. offered CMC services in 2011, and 1,205 companies in the U.S. offered Non-Clinical Research Services. The Clinical Research segment had 643 active companies in the U.S. providing services in 2011.

The majority — 69% — of contract R&D service providers overall are privately held companies. CMC and Non-Clinical Research services segments have the highest concentration of publicly traded companies at 47% and 52% respectively. Approximately 17% of all companies providing Clinical Research Services are public. Chart 3 depicts the proportion of public to private companies in each major U.S. contract R&D services market segment.

Applied Research Services and Other Services U.S. market segments are the least mature and most productive segments, as reflected in Table 1 and Table 2. Companies in the Applied Research Services segment are the youngest, the most likely to be privately held, and the smallest. As a more nascent segment, revenue per employee in the Applied Research Services segment is one of the highest, at $267,000. The Other Services segment is also relatively young, with a high concentration of privately held companies. Revenue per employee in this segment is higher than any other U.S. market segment, at $284,000.

Individual companies in the Clinical Research Services and Other Services segments generate more revenue per company and have relatively higher levels of employee productivity. The CMC and Non-Clinical Research Services segments are the most mature, with the highest proportion of publicly-traded companies, the highest average number of employees and the lowest relative employee productivity.

Discussion
This initial Tufts CSDD study sizes the overall U.S. contract R&D services using a systematic bottom-up approach based on actual company data whenever possible and imputed data based on benchmarked actuals. The overall U.S. market for the 15 highest concentration geographic areas — as defined by MSA — is estimated at between $32.5 and $39.5 billion. Assuming that these geographic areas represent 75% of the total U.S. market, and that the U.S. market contributes 50% of contract services worldwide, Tufts CSDD estimates that the total global market for all contract services supporting prescription drug R&D is $90 billion to $105 billion. The total global market for contract R&D services therefore is more than five times larger than commonly cited figures.

Adjusting the service areas to adhere to traditional market definitions established by the investment banking community, the Tufts CSDD figures for the Clinical Research and Preclinical Research markets are consistent with those published by financial analysts (see Table 3).

It is highly likely that the overall market and individual segment sizes are larger than the conservative estimates presented in this paper. Tufts CSDD acknowledges the limitations of usingHoovers.com to characterize the high proportion of privately held companies, as Hoovers tends to present ultra-conservative figures. In addition, there are some limitations to using imputed data within service area revenues, as there is a tendency to inflate the smallest company revenue. However, using our estimates combined with actual data from public and some private companies helps to mitigate this limitation to some degree.

The major market segment definitions and service areas that comprise them are a useful approach to organizing contract services companies and it may provide a valuable framework for future analyses. The Tufts CSDD study finds that all of the market segments are accommodating very large and highly diversified publicly traded companies and many small, specialty companies. CMC and Non-Clinical Research segments are the most mature with the oldest relative companies, the highest proportion publicly traded, and the lowest levels of employee productivity (e.g., revenue per employee). Segment maturity is a function of historical receptivity by pharmaceutical, biotechnology and medical device companies to outsource high fixed cost, manufacturing and labor-intensive activities that are deemed non-core. Relative to the other segments, the Clinical Research Services segment is one of the most productive with the highest proportion of privately held companies.

The Other Services segment remains too diverse, making it difficult to characterize this segment adequately. In the future, Tufts CSDD will look to refine the definition of this segment to ensure that it is a more homogeneous group of companies.

At the present time, Tufts CSDD is analyzing contract services company data by geographic cluster to better understand the economic impact of each market segment locally. In addition, Tufts CSDD plans to apply this more robust methodology to sizing the overall contract services market in Europe and in other major global regions.

Drug and device innovation is evolving and re-inventing itself continually. As R&D costs rise, operating and regulatory complexity increases, and mergers, acquisitions and consolidation continue, the use of contract service providers as integral and integrated sourcing providers will similarly continue to grow. It is our hope that the analysis and results contained in this article will play a role in improving future assessments of the size and structure of the outsourcing landscape.


Kenneth Getz, MBA, is Senior Research Fellow and Assistant Professor at Tufts Center for the Study of Drug Development. He can be reached at kenneth.getz@tufts.eduMary Jo Lamberti, Ph.D., is Senior Project Manager at Tufts CSDD. Stella Stergiopoulos is project manager, Tufts CSDD.  Adam Mathias is Research Analyst, Tufts CSDD. This project was funded by an unrestricted grant from the Kansas Bioscience Authority (KBA).

Source:

http://www.contractpharma.com/issues/2012-06/view_features/resizing-the-global-contract-rd-services-market/

US cities lose jobs and revenues as big

pharma companies close R&D facilities


By Tony Favro, USA Editor*

9 April 2012: 

In 2007, Pfizer, the pharmaceutical company, closed its research and development facility in Ann Arbor, Michigan, displacing 2100 workers. In 2009, the University of Michigan purchased the vacant site and expected to create two to three thousand jobs over ten years. At the time of the sale, Ann Arbor Mayor John Hieftje expressed mixed emotions. On the one hand, he said in a statement, “If the University of Michigan is able to greatly expand life sciences research in Ann Arbor it will have far-reaching long-term economic benefits for the whole region.” On the other hand, Mayor Hieftje told Crains’ Detroit Business newspaper, “[The deal] has troubling aspects for local government”. Hieftje was referring to the $14 million in local taxes paid by Pfizer, which will not continue since the University of Michigan is a tax-exempt organization.

• Profits versus R&D
• The Government steps in
• Shift in research culture
• Bigger government

The Ann Arbor story is not unique. According to the US Bureau of Labor Statistics, the pharmaceutical industry shed 35,000 in the United States in 2010, the most recent year for which complete data are available. Cities throughout the US were burdened by plant closures. Ann Arbor was luckier than most cities. The University of Michigan employed about 1,700 workers at the former Pfizer site at the end of 2011. These workers are doing much of the research formerly done by Pfizer — and this gets to the heart of the matter. Big pharma companies are abandoning basic drug research, leaving the federal government and universities to pick up the slack.

Profits versus R&D
According to the August 2011 issue of the journal Nature Reviews Drug Discovery, the decline of prescription drug research and development R&D is the result of 15 years of continuous industry consolidations and the drive by drug manufacturers to maximize profits.

Since 2000, for example, Pfizer has acquired three major drug makers, Warner-Lambert, Pharmacia, and Wyeth, closing research centers with each acquisition. “These [closed] sites housed thousands of scientists, and many major drugs were discovered there,” the journal notes. “The same pattern has been observed after most of the mergers and acquisitions by other major pharmaceutical companies during the past decade.”

Profit is another reason big pharma companies are abandoning basic research. Over the past couple of decades, big drug firms competed to produce blockbuster drugs that yielded huge payoffs. Drugs such as Merck’s Vioxx and Pfizer’s Lipitor generate several billion dollars in annual sales and reap big profits for their makers. The fierce competition leads to costly duplication of work with as many as 20 companies vying to be the first to come out with the next blockbuster drug. The stakes for drug companies become higher as patents expire for popular and profitable drugs and revenue streams dry up.

The potentially enormous profits of a breakthrough discovery, however, are proving too elusive to offset the heavy upfront costs of basic research and development, an estimated 10 to 20 per cent of total expenditures. As a researcher told the Rochester Business Journal, “The days of the blockbuster drug are over”.

Businesses survive by making money for their shareholders, and when part of a business can no longer reliably generate profits — in this case, basic drug research — the unprofitable part is understandably jettisoned.

This makes good business sense, but poor public policy. People need pharmaceuticals — in many instances, it’s a question of life or death — and so the federal government has had to fill the void left by drug companies’ retreat from basic and early-stage research.

The government steps in
Over the past few years, the federal National Institutes of Health has invested hundreds of millions of dollars to build a drug-discovery infrastructure. Most of the federal expenditures have been used to establish a network of 60 “clinical translational centers” at research universities. These centers are changing the direction of pharmaceutical research and creating new opportunities for public-private collaborations.

In essence, the emerging drug-development model in the USA has big pharmaceutical firms coming in at a later stage to market and distribute drugs that have been discovered and tested by university researchers and small, private biotech companies.

The emerging model promises to greatly expand opportunities for universities to earn royalties from pharmaceutical companies. The federal funding for “translational” research also incentivizes entrepreneurship at universities. Universities that develop and hold patents are expected to translate that knowledge into jobs, not only by contracting with big pharma but also by incubating and spinning-off small, private drug-development companies. In the federal model, big drug makers will strike licensing deals directly with universities or with small companies, primarily university spin-offs. One potential benefit of the new model is that entire categories of drugs previously ignored by big pharma because of their low-profitability may now be brought to market.

Shift in research culture
Federal monies are helping build a research infrastructure at the university level to bring basic discoveries to market as well as catalyze broader economic growth. This requires a culture shift at both universities and businesses. Traditionally, a scientific advance by a university professor might end as a research paper read by a few colleagues in the same field. In the clinical translational model supported by the National Institutes of Health, scientists must collaborate with colleagues in different fields — the chemist with the engineer and sociologist and marketing professor, for example. Drug companies also have to discuss their research and results with academics and with their counterparts at different drug firms. They can no longer label such information as proprietary and keep it to themselves.

Bigger government
Critics of big government should take note: when businesses contract, government often has to expand to protect citizens. Businesses may create jobs, but they will also pass their costs to taxpayers when they can. Large drug companies consider delivering a return to shareholders their first duty, and therefore cut R&D that drains short-term profits. But short-term business sense may threaten public health and even the profitability of corporations since, over the long-term, a less-healthy labor pool could drive up the cost of doing business.

And sometimes government requirements and mandates, such as the clinical translational research model, can spark economic growth. According to Dr. Karl Kieburtz of the University of Rochester, one of the first universities to be funded by the National Institutes of Health, “We are looking at many things, surgical devices and other things, not just drugs.” The University of Rochester, which purchased a building that Wyeth vacated for research, has already spun-off 30 companies. As multinational pharmaceutical companies unload more of their marginally-profitable but publicly-indispensible activities, the public and nonprofit sectors will have to fill the gap.

The effect on US city governments is uneven. Cities will lose jobs and property tax revenues when pharmaceutical companies close their R&D facilities. Cities fortunate enough to have a university with a translational research center should eventually recover their losses and more.

*Tony Favro also maintains the blog Planning and Investing in Cities.

Source:

http://www.citymayors.com/economics/usa_big_pharma_cities.html#Anchor-Profits-49575

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Reporter: Aviva Lev-Ari, PhD, RN

 

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– Jay Flatley, President and CEO, Illumina
– Lee Silver, Ph.D., Princeton University

Spanning three days, the conference will focus on:
– Day 1: Technology
– Day 2: Business + Translation
– Day 3: Application

And 40+ Cutting-Edge Presentations on:
– Personal Genomics
– Third-Generation Sequencing
– Molecular Diagnostics
– Investment & Funding Opportunities
– Genome Interpretation
– The Future of Personalized Medicine
– Big Data
– Prenatal/Neonatal & Disease Diagnostics
– Empowering Patients
– Nutrition, Food Genetics & Cosmetics

SPEAKERS

Confirmed speakers to date include:

Sandy Aronson, Executive Director of IT, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM)

Arindam Bhattacharjee, Ph.D., CEO and Founder, Parabase Genomics

Diana Bianchi, M.D., Executive Director, Mother Infant Research Institute; Vice Chair for Research, Department of Pediatrics, Floating Hospital for Children, Tufts Medical Center

Cinnamon Bloss, Ph.D., Assistant Professor and Director, Social Sciences and Bioethics, Scripps Translational Science Institute

Alexis Borisy, Partner, Third Rock Ventures

John Boyce, President and CEO, GnuBio

Mike Cariaso, Founder, SNPedia; Author of Promethease

Kenneth Chahine, Ph.D., J.D., Senior Vice President and General Manager, DNA, ancestry.com

Michael Christman, CEO, Coriell Institute for Medical Research

Cindy Crowninshield, RD, LDN, Licensed Registered Dietitian, Body Therapeutics & Sodexo; Founder, Eat2BeWell & Eat4YourGenes; Conference Director, Cambridge Healthtech Institute

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Chris Dwan, Principal Investigator and Director, Professional Services, BioTeam

Jay Flatley, President & CEO, Illumina

Andrew C. Fish, Executive Director, AdvaMedDx

Dennis Gilbert, Ph.D., Founder, President and CEO, VitaPath Genetics

Rosalynn Gill, Ph.D., Vice President, Clinical Affairs, Boston Heart Diagnostics

Steve Gullans, Managing Director, Excel Venture Management

Don Hardison, President & CEO, Good Start Genetics, Inc.

Richard Kellner, Founder and President, Genome Health Solutions, Inc.

Robert Klein, Ph.D., Chief Business Development Officer, Complete Genomics

Isaac S. Kohane, M.D., Ph.D., Henderson Professor of Health Sciences and Technology, Children’s Hospital and Harvard Medical School; Director, Countway Library of Medicine; Director, i2b2 National Center for Biomedical Computing; Co-Director, HMS Center for Biomedical Informatics

Stan Lapidus, President, CEO and Founder, SynapDx

Gholson Lyon, M.D., Ph.D., Assistant Professor in Human Genetics, Cold Spring Harbor Laboratory; Research Scientist, Utah Foundation for Biomedical Research

Daniel MacArthur, Ph.D., Assistant Professor, Massachusetts General Hospital; Co-founder, Genomes Unzipped

Craig Martin, Chief Executive Officer, Feinstein Kean Healthcare

James McCullough, CEO and Founder, Exosome Diagnostics

Kevin McKernan, CSO, Courtagen Life Sciences

Neil A. Miller, Director of Informatics, Center for Pediatric Genomic Medicine, Children’s Mercy Hospital

Paul Morrison, Ph.D., Laboratory Director, Molecular Biology Core Facilities, Dana-Farber Cancer Institute

Geert-Jan Mulder, M.D., General Partner, Forbion Capital

Steve Murphy, M.D., Managing Partner, Wellspring Total Health

Michael Murray, M.D., Clinical Chief, Genetics Division, Brigham and Women’s Hospital; Instructor, Harvard Medical School, The Harvard Clinical and Translational Science Center

Brian T. Naughton, Ph.D., Founding Scientist, 23andMe

Nathan Pearson, Ph.D., Director of Research, Knome, Inc.

Michael S. Phillips, Ph.D., Canada Research Chair in Translational Pharmacogenomics; Director, Molecular Diagnostic Laboratory, Montreal Heart Institute; Associate Professor, Université de Montréal

John Quackenbush, Ph.D., Professor, Biostatistics and Computational Biology, Cancer Biology Center for Cancer Computational Biology, Dana-Farber Cancer Institute

Martin G. Reese, President and CEO, Omicia

Heidi L. Rehm, Ph.D., FACMG, Chief Laboratory Director, Molecular Medicine, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM); Assistant Professor of Pathology, Harvard Medical School

Oliver Rinner, Ph.D., CEO, BiognoSYS AG

Meredith Salisbury, Senior Consultant, Bioscribe

Marc Salit, Group Leader, Biochemical Science and Multiplexed Biomolecular Science, National Institute of Standards and Technology

Lee Silver, Ph.D., Professor of Molecular Biology and Public Affairs; Faculty Associate, Science, Technology & Environmental Policy Program, Office of Population Research, and the Center for Health and Wellbeing, Woodrow Wilson School, Princeton University

Jamie Streator, Managing Director, Healthcare Investment Banking, Cowen & Company

Joseph V. Thakuria, M.D., MMSc, Attending Physician in Clinical and Biochemical Genetics Medical Genetics, Massachusetts General Hospital; Medical Director, Personal Genome Project; Harvard Catalyst Translational Genetics and Bioinformatics Program, MGH Center for Human Genetics Research

Samuil R. Umansky, M.D., Ph.D., D.Sc., Co-founder, CSO, and President, DiamiR LLC

David A. Weitz, Ph.D., Mallinckrodt Professor of Physics and Applied Physics, Harvard School of Engineering and Applied Sciences

Speaker to be Announced, Barclays

DAY 1: TECHNOLOGY

WEDNESDAY, OCTOBER 3

7:30 am Conference Registration

8:30 Opening Remarks

John Boyce, President and CEO, GnuBIO and Meredith Salisbury, Senior Consultant, Bioscribe

 

OPENING PLENARY SESSION

 

» 8:45 KEYNOTE PRESENTATION

Self-Discovery in the Age of Personal Genomes

Lee Silver, Ph.D., Professor of Molecular Biology and Public Affairs; Faculty Associate, Science, Technology & Environmental Policy Program, Office of Population Research, and the Center for Health and Wellbeing, Woodrow Wilson School, Princeton University

With blinding speed, the biomedical research enterprise is advancing the technology to read personal genomes with greater accuracy, in less time, and at less expense.Meanwhile, consumer genetics has blossomed from infancy to adolescence with an array of innovative consumer-facing products. This unanticipated cottage industry is struggling with growing pains in a mix of conflicted regulators, restless innovators, and demanding consumers. Genetic information, like all information, “wants to be free,” but the commercialization environment is not yet optimized for personal freedom.

 

9:40 The Era of Clinical Sequencing and Personalized Medicine

Michael Christman, CEO, Coriell Institute for Medical Research

Advances in understanding genomic variation and associated clinical phenotypes continue to increase while the cost of full genome sequencing rapidly declines. Having access to your genomic information will become increasingly important as physicians are progressively receptive to incorporating genomics into routine clinical practice. When you need a new prescription, it will be necessary for your physician to quickly and securely access your genetic data to understand drug efficacy prior to dosing. Who will patients and medical professionals trust to store and interpret the data? Coriell is positioned to significantly contribute to the research needed to accelerate the adoption and routine use of genomics in medicine.

 

10:20 FEATURED PRESENTATION

Stan Lapidus, President, CEO and Founder, SynapDx

 

10:50 Coffee Break

 

BIG DATA/ANALYSIS

11:20 IT Infrastructure Required to Manage Patient Genetic Test Results

Sandy Aronson, Executive Director of IT, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM)

There are many challenges associated with getting the maximum value out of a genetic test. This talk will focus on information technology infrastructure that can help.

11:50 Issues in Genomics at Scale

Chris Dwan, Principal Investigator and Director, Professional Services, BioTeam

2012 marks, in many respects, the beginning of the second decade of high-throughput DNA sequencing. Robust, well understood solutions exist for many of the major technical challenges involved in operating a high-throughput genomics facility. Petabyte scale data storage, well suited to research computing in this space, provides a clean example. Certainly it still requires careful planning and thorough engineering to deploy such infrastructure. However, we can now purchase robust systems from multiple vendors rather than having to stitch together solutions in-house. Perhaps more importantly, we can rely on the experience of a community of peers who have been through the exercise before. By contrast, the legal, regulatory, ethical, and privacy concerns in this space have only begun to be explored. As we plan for the coming years, we must certainly plan for technical uncertainty. Technologists find themselves in the role of guessing at the future. As translational medicine, clinical genome sequencing, and other practices become the norm, we must assume extreme and occasionally capricious changes to the social ecosystem. This talk will explore these issues in the context of nearly a decade supporting research computing and genomics for a broad variety of institutions.

12:20 pm Sponsored Presentation (Opportunity Available)

12:50 Luncheon Presentation (Sponsorship Opportunity Available)
or Lunch on Your Own

 

MOLECULAR DIAGNOSTICS

2:05 Panel Discussion
Panelists will first give a brief presentation and then convene for a panel discussion.

Michael S. Phillips, Ph.D., Canada Research Chair in Translational Pharmacogenomics; Director, Molecular Diagnostic Laboratory, Montreal Heart Institute; Associate Professor, Université de Montréal (Moderator)

Molecular Diagnostics and the Patient/Consumer

Andrew C. Fish, Executive Director, AdvaMedDx

This presentation will envision a future in which molecular diagnostics are widely utilized not only for decision making by health professionals, but also for the development and use of a wide range of consumer products that include genetic tests themselves. The speaker will discuss various policy implications of this convergence of patient and consumer interests driven by the expanding availability of molecular diagnostics.

Bridging the Gap between Genetic Risk and Blood Diagnostics by Personalized Health Monitoring

Oliver Rinner, Ph.D., CEO, Biognosys AG

Biognosys has developed a solution to quantify and track protein levels over time from a drop of blood. With a novel mass spectrometric technology, we can record protein signals from 1000s of proteins in a single instrument run and store such digital protein maps in a digital bio-bank that can be screened in silico for known and novel biomarkers. We will provide this technology as personalized health monitoring to patients and consumers that seek actionable information about their state of health.

Measuring Disease Treatment and Progression at the Molecular Level without Biopsy

James McCullough, CEO and Founder, Exosome Diagnostics

Exosome has developed a solution that has the ability to measure, at the molecular level without biopsy, the dynamic nature of both treatment and disease progression. The company has developed a means of isolating exosomes: exosomes are shed into all biofluids, including blood, urine, and CSF, forming a stable source of intact, disease-specific nucleic acids. From these, the company is able to develop predictive gene expression profiles to achieve high sensitivity for rare gene transcripts and the expression of genes responsible for cancers and other diseases. This technology obviates the need for biopsy, and provides a means for detection at a much earlier stage of treatment.

3:20 Refreshment Break

3:50 Sponsored Presentation (Opportunity Available)

 

SEQUENCING

4:20 Panel Discussion

Like a double helix, the future growth of consumer genetics is intimately entwined with technology advances in next-generation sequencing. While the industry excitedly awaits the commercial debut of potentially disruptive nanopore sequencing platforms, existing platforms continue to roll out new enhancements and sequencing strategies that bring us within striking distance of clinical-grade whole genome sequencing. This panel discussion brings together leaders from existing and emerging sequencing providers to present and debate a range of questions including the pros and cons of targeted versus whole-genome sequencing, the emergence of third-generation sequencing platforms, and the challenges of integrating genome sequencing into the clinic.

Paul Morrison, Ph.D., Laboratory Director, Molecular Biology Core Facilities, Dana-Farber Cancer Institute (Moderator)

Panelists:

John Boyce, President and CEO, GnuBIO
Robert Klein, Ph.D., Chief Business Development Officer, Complete Genomics Inc.
Speaker to be Announced, Life Technologies
Speaker to be Announced, Illumina

5:50-6:50 Welcome Reception in the Exhibit Hall with Poster Viewing

 

DAY 2: BUSINESS + TRANSLATION

THURSDAY, OCTOBER 4

7:45 am Morning Coffee

 

TRANSLATIONAL GENOMICS

8:15 Panel Discussion
Panelists will first give a brief presentation and then convene for a panel discussion.

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World (Moderator)

All Genomes are Dysfunctional: The Challenges of Interpreting Whole-Genome Data from Healthy Individuals

Daniel MacArthur, Ph.D., Assistant in Genetics, Massachusetts General Hospital; Co-founder, Genomes Unzipped

Recent advances in DNA sequencing technology have made cheap, rapid interrogation of complete genome and exome sequences an almost mundane exercise, and have resulted in significant progress in the discovery of disease-causing sequence changes from the genomes of individuals with rare diseases or cancers. However, such successes do not necessarily translate into an improved ability to use genome-scale data to predict future disease probability for currently healthy individuals. In this presentation I will highlight some of the major technical and analytical challenges associated with developing predictive genomic medicine for the healthy majority.

Consumer Genomics: What do People do with Their Genomes?

Cinnamon Bloss, Ph.D., Assistant Professor and Director, Social Sciences and Bioethics, Scripps Translational Science Institute

Direct-to-consumer personalized genomic testing is controversial, and there are few empirical data to inform the debate regarding use and regulation. The Scripps Genomic Health Initiative is a large longitudinal cohort study of over 2,000 adults who have undergone testing with a commercially available genomic test. Findings from this initiative regarding the psychological, behavioral and clinical impacts of genomic testing on consumers will be presented.

Advances in Noninvasive Prenatal Genetic Testing: Does this Mean “Designer” Babies for All?

Diana Bianchi, M.D., Executive Director, Mother Infant Research Institute; Vice Chair for Research, Department of Pediatrics, Floating Hospital for Children, Tufts Medical Center

Noninvasive prenatal testing for Down syndrome and other chromosome disorders using massively parallel DNA sequencing techniques is now available on a clinical basis in the US. With expected advances in sequencing techniques it will soon be possible to take a blood sample from a pregnant woman and determine if her fetus has a chromosome abnormality or a single gene disorder. How much information do prospective couples want and how do these technical advances affect well-established algorithms for prenatal care?

Translating Genomics into Clinical Care

Heidi L. Rehm, Ph.D., FACMG, Chief Laboratory Director, Molecular Medicine, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM); Assistant Professor of Pathology, Harvard Medical School

This talk will focus on approaches to integrate clinical sequencing into genomic medicine. It will cover next generation sequencing test development from disease panels to whole genomes and the interpretation and reporting of genetic variants identified in patients.

Impact of Genomic Sequencing on Public Health and Preventive Medicine

Joseph V. Thakuria, M.D., MMSc, Attending Physician in Clinical and Biochemical Genetics and Medical Director, Personal Genome Project, Massachusetts General Hospital Center for Human Genetics Research

Early findings in the Personal Genome Project (established by George Church) suggest significant impact for public health and preventive medicine. Solutions to accelerate clinical adoption and address large molecular data challenges will be explored.

9:30 FEATURED PRESENTATION
Genome-in-a-Bottle: Reference Materials and Methods for Confidence in Whole Genome Sequencing

Marc Salit, Group Leader, Biochemical Science and Multiplexed Biomolecular Science, National Institute of Standards and Technology

Genome-in-a-Bottle: Reference Materials and Methods for Confidence in Whole Genome Sequencing Clinical application of ultra high throughput sequencing (UHTS) or “Next Generation Sequencing” for hereditary genetic diseases and oncology is rapidly emerging.  At present, there are no widely accepted genomic standards or quantitative performance metrics for confidence in variant calling. These are needed to achieve the confidence in measurement results expected for sound, reproducible research and regulated applications in the clinic.  NIST has convened the “Genome-in-a-Bottle Consortium” to develop the reference materials, reference methods, and reference data needed to assess confidence in human whole genome variant calls. A principal motivation for this consortium is to develop an infrastructure of widely accepted reference materials and accompanying performance metrics to provide a strong scientific foundation for the development of regulations and professional standards for clinical sequencing.

10:00 Coffee Break in the Exhibit Hall with Poster Viewing

 

VENTURE CAPITAL & INVESTMENT BANKING

10:30 Panel Discussion

This “Funding to IPO Panel” consists of some of the top venture capitalists and investment bankers in therapeutics, diagnostics, and consumer genetics. This series of presentations and follow-on panel, will take attendees through the financial cycle – from funding to IPO, with VC’s and bankers highlighting the corporate criteria most important to them, and the metrics by which they make their decisions.
Panelists:

Geert-Jan Mulder, M.D., General Partner, Forbion Capital

Alexis Borisy, Partner, Third Rock Ventures

Steve Gullans, Managing Director, Excel Venture Management

Jamie Streator, Managing Director, Healthcare Investment Banking, Cowen & Company

Speaker to be Announced, Barclays

12:15 pm Luncheon Presentation (Sponsorship Opportunity Available)
or Lunch on Your Own

 

GENOME DATA: THE PHYSICIAN’S PERSPECTIVE

1:45 Panel Discussion

While making the effort to deploy genomics and sequence data in preventative and clinical care is a noble cause, it is also one that requires pragmatic solutions. This panel discussion will address practical issues related to the day-to-day use of genomic technologies in the clinic — from hospital to private practice to academia.

Steve Murphy, M.D., Managing Partner, Wellspring Total Health (Moderator)
Panelists:

Michael Murray, M.D., Clinical Chief, Genetics Division, Brigham and Women’s Hospital; Instructor, Harvard Medical School, The Harvard Clinical and Translational Science Center

Isaac Samuel Kohane, M.D., Ph.D., Henderson Professor of Health Sciences and Technology, Children’s Hospital and Harvard Medical School; Director, Countway Library of Medicine; Director, i2b2 National Center for Biomedical Computing; Co-Director, HMS Center for Biomedical Informatics

3:00 Refreshment Break in the Exhibit Hall with Poster Viewing

 

GENOME INTERPRETATION

3:30 Omicia: Interpreting Genomes for Clinical Relevance

Martin G. Reese, President and CEO, Omicia

Automatic annotation of variants and integration of disparate data sources is just the first step in the eventual adoption of genomes into clinical practice. The next step is reducing this complexity into the very few, actionable clinically relevant findings. We will show how we integrate such methods within an automated, comprehensive and easy-to-use platform for the interpretation of individual genome data. This system allows for prioritizing variants with respect to its potential clinical impact and is preloaded with clinical gene sets and proprietary annotations to enhance discovery and reporting of personal genes and variants. Furthermore, it is extensible and allows the integration of the user’s proprietary gene and variants sets. We will show several exome and genome analyses.

3:50 Personalized Genomic Interpretation with SNPedia and Promethease

Mike Cariaso, Founder, SNPedia; Author of Promethease

With whole genome prices falling and microarray genotyping accessible to ordinary people over the internet, the challenge is no longer in acquiring the raw data, but in interpreting and using it. In this talk, I will outline a freely available database of literature, organized by the relevant DNA position and phenotypic effects. A complementary analysis program reads raw genomic data and produces a hyperlinked and searchable report of known associations. It can also perform special processing of family trios (child, mother, father), make predictions about offspring, and identify shared ancestry.

4:10 GenoSpace: Creating an Information Ecosystem for 21st Century Genomic Medicine

John Quackenbush, Ph.D., Professor, Biostatistics and Computational Biology, Cancer Biology Center for Cancer Computational Biology, Dana-Farber Cancer Institute

New sequencing technologies are driving the cost of genomic data generation to unprecedented lows, making sequencing available as a potentially valuable clinical and diagnostic tool. The challenge is solving “the last 100 yards” problem–delivering the data to those who need to access it in a manner in which they can use it effectively. GenoSpace has developed technology to connect the diverse consumers and producers of genomic data, creating an ecosystem in which we have the potential to advance genomic medicine.

 

VISIONS FOR PERSONALIZED MEDICINE

 

» 4:30 KEYNOTE PRESENTATION

The Big Picture: Visions for Personalized Medicine

Jay Flatley, President and CEO, Illumina

 

Illumnia logo small5:30 Social Event and Party

 

DAY 3: APPLICATIONS

FRIDAY, OCTOBER 5

8:00 am Morning Coffee

» 8:30 KEYNOTE PRESENTATION 

An Inside Look at How AncestryDNA Uses Population Genetics to Enrich Its Online Family History Experience

Kenneth Chahine, Ph.D., J.D., Senior Vice President & General Manager, DNA, ancestry.com

Ancestry.com is the world’s largest online resource for family history with an extensive collection of over 10 billion historical records that are digitized, indexed and made available online over the past 13 years. In May 2012, AncestryDNA launched a direct-to-consumer genealogical DNA test that delivers two results to customers. The first result predicts identity-by-descent and allows the customer to find genetic relatives within the AncestryDNA customer database. The second determines the customer’s admixture to provide a predicted genetic ethnicity using a state-of-the-art algorithm. The AncestryDNA team leverages pedigrees, documents, geographical information and its extensive biobank of worldwide DNA samples to conduct innovative research in population genetics and translates the complexities of genetic science into a simple, understandable, and meaningful user experience.

 

9:15 Past, Present and Future of Consumer Genetics, a Pioneer’s Perspective

Rosalynn Gill, Ph.D., Vice President, Clinical Affairs, Boston Heart Diagnostics

The first consumer genetics company, Sciona, founded by Rosaylnn Gill, launched its services in April 2001 in the UK in what was either a breakthrough in innovation or an act of incredible naiveté. Twelve years later, many lessons have been learned, but the jury is still out on the appropriate regulatory framework, the necessary industry standards and what constitutes a sustainable business model.

9:45 Sponsored Presentation (Opportunity Available)

10:15 Coffee Break in the Exhibit Hall with Poster Viewing

 

PRENATAL/NEONATAL DIAGNOSTICS 

10:45 Panel Discussion

Panelists will first give a brief presentation and then convene for a panel discussion.

Meredith Salisbury, Senior Consultant, Bioscribe (Moderator)

Neonatal Genomic Medicine

Neil A. Miller, Director of Informatics, Center for Pediatric Genomic Medicine, Children’s Mercy Hospital

The causal gene is known for more than 3,500 monogenic diseases. Many of these can present in the neonatal period, causing up to 30% of neonatal intensive care unit admissions. In the last six months, we have started to offer very rapid diagnostic testing for these diseases at Children’s Mercy Hospital based on genome sequencing. The emerging indications and utility of neonatal genomic medicine will be discussed.

Screening Neonates by Targeted Next-Generation DNA Sequencing

Arindam Bhattacharjee, Ph.D., CEO and Founder, Parabase Genomics

We are developing a neonatal genome sequencing test that will allow screening and diagnosis of primarily newborns and infants affected with a disease or condition allowing prompt treatment. The current approach of DNA based genetic screening for symptomatic and high-risk is not focused around neonates, and so healthcare providers and parents are unable to understand the cause and treatment of the condition in absence of clear symptoms. Our test is unique in that it simultaneously screens and/or diagnoses hundreds of these conditions at once from a single sample, providing more comprehensive information to families and their physicians. It is yet affordable, and provides access to the high-resolution sequence data.

Using NGS Sequencing to Improve the Standard of Care for Routine Genetic Carrier Screening

Don Hardison, President & CEO, Good Start Genetics, Inc.

11:45 Luncheon Presentation (Sponsorship Opportunity Available)
or Lunch on Your Own

 

NUTRITION, FOOD GENETICS & COSMETICS

1:00 The Importance of Genetic Testing-Directed Vitamin Use

Dennis Gilbert, Ph.D., Founder, President and CEO, VitaPath Genetics

VitaPath Genetics, Inc. has developed a platform for genomic-based tests that determine the need for vitamin therapy in medically actionable conditions. Using its platform, VitaPath can develop specific vitamin-remediated risk assays that help manage the use of the $30 billion spent on supplements in the U.S. each year. The first test developed by VitaPath measures genetic risk factors associated with the spina bifida to identify women who would benefit from low-risk, prescription strength folic acid supplementation.

1:20 Using Weight Management Genetic Testing in Nutrition Counseling:
A Dietitian Weighs in on the Matter

Cindy Crowninshield, RD, LDN, Licensed Registered Dietitian, Body Therapeutics & Sodexo; Founder, Eat2BeWell & Eat4YourGenes; Conference Director, Cambridge Healthtech Institute

Between January-July 2012, 15 patients took a weight management genetic test to support their weight loss efforts. An individualized nutrition plan based on their eating and lifestyle habits and test results was created for each person. Data and several case studies will be presented to show how successful these patients were in achieving their weight loss goals. Challenges and opportunities will be discussed. Also presented will be tips and suggestions for genetic testing companies on how they can work best with a private practitioner’s office.

1:40 How Microfluidics is Changing the Landscape of Personalized Cosmetics

David A. Weitz, Ph.D., Mallinckrodt Professor of Physics and Applied Physics, Harvard School of Engineering and Applied Sciences

2:00 Refreshment Break in the Exhibit Hall with Poster Viewing

 

DISEASE DIAGNOSTICS

2:30 Clinical Sequencing and Mitochondrial Disease

Kevin McKernan, CSO, Courtagen Life Sciences

We describe the results from sequencing 64 patients’ Mitochondrial genomes in conjunction with 1,100 nuclear genes. Complementing this data with multiplex ELISA assays to monitor protein levels in the blood can provide additional insight to variants of unknown significance and aid therapeutic decisions.

2:50 A Paradigm Shift: Universal Screening Test

Samuil R. Umansky, M.D., Ph.D., D.Sc., Co-founder, CSO, and President, DiamiR LLC

We will present a fundamentally new approach to the development of a screening test aimed at diseases of various organ systems, organs and tissues. The test is non-invasive and cost efficient. The data we will present demonstrate the potential of our approach for early detection of neurodegenerative diseases, cancer and inflammatory diseases of gastrointestinal and pulmonary systems.

 

THE EMPOWERED PATIENT

3:10 Genomes R Us – How Personalized Medicine is Reshaping the Role of Patients, and Why It Matters

Craig Martin, CEO, Feinstein Kean Healthcare

Much has been said about the advancements in science underlying the genomic revolution. We are beginning now to see the impact at the clinical level, and there’s more to come in the pipeline. But what does this shift in medicine do to change the role of the patient? This presentation provides insights into how best to engage with patient communities to expedite research, commercialization and market impact of innovative technologies, diagnostics and treatments, and to help validate the relative efficacy of such advancements in a value-driven world.

3:40 Consumer Empowerment in Health Care and Personal Genomics: Ethical, Societal and Regulatory Considerations

Gholson Lyon, M.D., Ph.D., Assistant Professor in Human Genetics, Cold Spring Harbor Laboratory; Research Scientist, Utah Foundation for Biomedical Research

The pace of exome and genome sequencing is accelerating with the identification of many new disease-causing mutations in research settings, and it is likely that whole exome or genome sequencing could have a major impact in the clinical arena in the relatively near future. However, the human genomics community is currently facing several challenges, including phenotyping, sample collection, sequencing strategies, bioinformatics analysis, biological validation of variant function, clinical interpretation and validity of variant data, and delivery of genomic information to various constituents. I will review these challenges, with an eye toward consumer genetics.

4:10 It Hurts Less If You Know More: An Empowered Patient’s Diagnostic Odyssey

Richard Kellner, Co-Founder and President, Genome Health Solutions, Inc.

For the early detection, diagnosis and treatment of cancer, there is a wide gap between current “standards of care” and what is possible through the use of advanced genomic technologies. Over the past two years I learned this lesson first hand through personal experiences involving myself, close friends and family members. My story is one of serendipity, frustration and then hope. I learned that, unfortunately, where you live and who you know can greatly influence your quality of care. I also learned that you can overcome these limitations by becoming an “empowered patient” who actively seeks out doctors who are willing to get outside of their comfort zones and practice “participatory medicine,” sometimes at the cutting edge of new precision diagnostics. I will present a new roadmap that both patients and doctors can follow toward a new era of personalized genomic medicine.

 

COMPANIES THAT EMPOWER THE PATIENT

4:40 23andMe’s DTC Exome

Brian T. Naughton, Ph.D., Founding Scientist, 23andMe

In October 2011, 23andMe launched a $999 direct-to-consumer exome product to a limited group of customers.This talk presents findings from this project, including the ubiquitous issue of variants of unknown significance.

5:10 Winding the Asklepian Wand: The Advent of Whole Genomes in Healthcare

Nathan Pearson, Ph.D., Director of Research, Knome, Inc.

With ever cheaper sequencing, richer reference data, and sharper interpretation methods, the clinical use of whole genomes is taking root in pediatrics, oncology, and beyond. Our genomes will ultimately join other cornerstones of clinical care, helping us stay healthier from birth to old age. But that prospect will require fast, robust pipelines that smartly interpret genomes, in the context of good phenotype data, and feed decisive insights back to patients and caregivers. Learn how Knome is making that happen.

5:40 Close of Conference

Source:

http://www.consumergeneticsconference.com/cgc_content.aspx?id=117407&libID=117355

 

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Reporter: Aviva Lev-Ari, PhD, RN

Genomics and the State of Science Clarity

Projects supported by the US National Institutes of Health will have produced 68,000 total human genomes — around 18,000 of those whole human genomes — through the end of this year, National Human Genome Research Institute estimates indicate. And in his book, The Creative Destruction of Medicine, the Scripps Research Institute‘s Eric Topol projects that 1 million human genomes will have been sequenced by 2013 and 5 million by 2014.

“There’s a lot of inventory out there, and these things are being generated at a fiendish rate,” says Daniel MacArthur, a group leader in Massachusetts General Hospital‘s Analytic and Translational Genetics Unit. “From a capacity perspective … millions of genomes are not that far off. If you look at the rate that we’re scaling, we can certainly achieve that.”

The prospect of so many genomes has brought clinical interpretation into focus — and for good reason. Save for regulatory hurdles, it seems to be the single greatest barrier to the broad implementation of genomic medicine.

But there is an important distinction to be made between the interpretation of an apparently healthy person’s genome and that of an individual who is already affected by a disease, whether known or unknown.

In an April Science Translational Medicine paper, Johns Hopkins University School of Medicine‘s Nicholas Roberts and his colleagues reported that personal genome sequences for healthy monozygotic twin pairs are not predictive of significant risk for 24 different diseases in those individuals. The researchers then concluded that whole-genome sequencing was not likely to be clinically useful for that purpose. (See sidebar, story end.)

“The Roberts paper was really about the value of omniscient interpretation of whole-genome sequences in asymptomatic individuals and what were the likely theoretical limits,” says Isaac Kohane, chair of the informatics program at Children’s Hospital Boston. “That was certainly an important study, and it was important to establish what those limits of knowledge are in asymptomatic populations. But, in fact, the major and most important use cases [for whole-genome sequencing] may be in cases of disease.”

Still, targeted clinical interpretations are not cut and dried. “Even in cases of disease, it’s not clear that we know now how to look across multiple genes and figure out which are relevant, which are not,” Kohane adds.

While substantial progress has been made — in particular, for genetic diseases, including certain cancers — ambiguities have clouded even the most targeted interpretation efforts to date. Technological challenges, meager sample sizes, and a need for increased, fail-safe automation all have hampered researchers’ attempts to reliably interpret the clinical significance of genomic variation. But perhaps the greatest problem, experts say, is a lack of community-wide standards for the task.

Genes to genomes

When scientists analyzed James Watson’s genome — his was the first personal sequence, completed in 2007 and published in Nature in 2008 — they were surprised to find that he harbored two putative homozygous SNPs matching Human Gene Mutation Database entries that, were they truly homozygous, would have produced severe clinical pheno-types.

But Watson was not sick.

As researchers search more and more genomes, such inconsistencies are increasingly common.

“My take on what has happened is that the people who were doing the interpretation of the raw sequence largely were coming from a SNPs world, where they were thinking about sequence variants that have been observed before, or that have an appreciable frequency, and weren’t thinking very much about the single-ton sequence variants,” says Sean Tavtigian, associate professor of oncology at the University of Utah.

“There is a qualitative difference between looking at whole-genome sequences and looking at single genes or, even more typically, small numbers of variants that have been previously implicated in a disease,” Boston’s Kohane adds.
“Previously, because of the cost and time limitations around sequencing and genotyping, we only looked at variants in genes for which we had a clinical indication. Now, since we can essentially see that in the near future we will be able to do a full genome sequence for essentially the same cost as just a focused set-of-variants test, all of the sudden we have to ask ourselves: What is the meaning of variants that fall outside where we would have ordinarily looked for a given disease or, in fact, if there is no disease at all?”

Mass General’s MacArthur says it has been difficult to pinpoint causal variants because they are enriched for both sequencing and annotation errors. “In the genome era, we can generate those false positives at an amazing rate, and we need to work hard to filter them back out,” he says.

“Clinical geneticists have been working on rare diseases for a long time, and have identified many genes, and are used to working in a world where there is sequence data available only from, say, one gene with a strong biological hypothesis. Suddenly, they’re in this world where they have data from patients on all 20,000 genes,” MacArthur adds. “There’s a fundamental mind-shift there, in shifting from one gene through to every gene. My impression is that the community as a whole hasn’t really internalized that shift; people still have a sense in their head that if you see a strongly damaging variant that segregates with the disease, and maybe there’s some sort of biological plausibility around it as well, that that’s probably the causal variant.”

Studies have shown that that’s not necessarily so. Because of this, “I do worry that in the next year or so we’ll see increasing numbers of mutations published that later prove to just be benign polymorphisms,” MacArthur adds.

“The meaning of whole-genome -sequence I think is very much front-and-center of where genomics is going to go. What is the true, clinical meaning? What is the interpretation? And, there’s really a double-edged sword,” Kohane says. On one hand, “if you only focus on the genes that you believe are relevant to the condition you’re studying, then you might miss some important findings,” he says. Conversely, “if you look at every-thing, the likelihood of a false positive becomes very, very high. Because, if you look at enough things, invariably you will find something abnormal,” he adds.

False positives are but one of the several challenges scientists working to analyze genomes in a clinical context face.

Technical difficulties

That advances in sequencing technologies are far outstripping researchers’ abilities to analyze the data they produce has become a truism of the field. But current sequencing platforms are still far from perfect, making most analyses complicated and nuanced. Among other things, improvements in both read length and quality are needed to enable accurate and reproducible interpretations.

“The most promising thing is the rate at which the cost-per-base-pair of massively parallel sequencing has dropped,” Utah’s Tavtigian says. Still, the cost of clinical sequencing is not inconsequential. “The $1,000, $2,000, $3,000 whole-genome sequences that you can do right now do not come anywhere close to 99 percent probability to identify a singleton sequence variant, especially a biologically severe singleton sequence variant,” he says. “Right now, the real price of just the laboratory sequencing to reach that quality is at least $5,000, if not $10,000.”

However, Tavtigian adds, “techniques for multiplexing many samples into a channel for sequencing have come along. They’re not perfect yet, but they’re going to improve over the next year or so.”

Using next-generation sequencing platforms, researchers have uncovered a variety of SNPs, copy-number variants, and small indels. But to MacArthur’s mind, current read lengths are not up to par when it comes to clinical-grade sequencing, and they have made supernumerary quality-control measures necessary.

“There’s no question that we’re already seeing huge improvements. … And as we add in to that changes in technology — for instance much, much longer sequencing reads, more accurate reads, possibly combining different platforms — I think these sorts of [quality-control] issues will begin to go away over the next couple of years,” MacArthur says. “But at this stage, there is still a substantial quality-control component in any sort of interpretation process. We don’t have perfect genomes.”

In a 2011 Nature Biotechnology paper, Stanford University’s Michael Snyder and his colleagues sought to examine the accuracy and completeness of single-nucleotide variant and indel calls from both the Illumina and Complete Genomics platforms by sequencing the genome of one individual using both technologies. Though the researchers found that more than 88 percent of the unique single-nucleotide variants they detected were concordant between the two platforms, only around one-quarter of the indel calls they generated matched up. Overall, the authors reported having found tens of thousands of platform-specific variant calls, around 60 percent of which they later validated by genotyping array.

For clinical sequencing to ever become widespread, “we’re going to have to be able to show the same reproducibility and test characteristic modification as we have for, let’s say, an LDL cholesterol level,” Boston’s Kohane says. “And if you measure it in one place, it should not be too different from another place. … Even before we can get to the clinical meaning of the genomes, we’re going to have to get some industry-wide standards around quality of sequencing.”
Scripps’ Topol adds that when it comes to detecting rare variants, “there still needs to be a big upgrade in accuracy.”

Analytical issues

Beyond sequencing, technological advances must also be made on the analysis end. “The next thing, of course, is once you have better -accuracy … being able to do all of the analytical work,” Topol says. “We’re getting better at the exome, but every-thing outside of protein-coding -elements, there’s still a tremendous challenge.”

Indeed, that challenge has inspired another — a friendly competition among bioinformaticians working to analyze pediatric genomes in a pedigree study.

With enrollment closed and all sequencing completed, participants in the Children’s Hospital Boston-sponsored CLARITY Challenge have rolled up their shirtsleeves and begun to dig into the data — de-identified clinical summaries and exome or whole-genome sequences generated by Complete Genomics and Life Technologies for three children affected by rare diseases of unknown genetic basis, and their parents. According to its organizers, the competition aims to help set standards for genomic analysis and interpretation in a clinical setting, and for returning actionable results to clinicians and patients.

“A bunch of teams have signed up to provide clinical-grade reports that will be checked by a blue-ribbon panel of judges later this year to compare and contrast the different forms of clinical reporting at the genome-wide level,” Kohane says. The winning team will be announced this fall and will receive a $25,000 prize, he adds.

While the competition covers all aspects of clinical sequencing — from readout to reporting — it is important to recognize that, more generally, there may not be one right answer and that the challenges are far-reaching, affecting even the most basic aspects of analysis.

“There is a lot of algorithm investment still to be made in order to get very good at identifying the very rare or singleton sequence variants from the massively parallel sequencing reads efficiently, accurately, [and with] sensitivity,” Utah’s Tavtigian says.

Picking up a variant that has been seen before is one thing, but detecting a potentially causal, though as-yet-unclassified variant is a beast of another nature.

“Novel mutations usually need extensive knowledge but also validation. That’s one of the challenges,” says Zhongming Zhao, associate professor of biomedical informatics at Vanderbilt University. “Validation in terms of a disease study is most challenging right now, because it is very time-consuming, and usually you need to find a good number of samples with similar disease to show this is not by chance.”

Search for significance

Much like sequencing a human genome in the early- to mid-2000s was more laborious than it is now, genome interpretation has also become increasingly automated.

Beyond standard quality-control checks, the process of moving from raw data to calling variants is now semiautomatic. “There’s essentially no manual intervention required there, apart from running our eyes over [the calls], making sure nothing has gone horribly wrong,” says Mass General’s MacArthur. “The step that requires manual intervention now is all about taking that list of variants that comes out of that and looking at all the available biological data that exists on the Web, [coming] up with a short-list of genes, and then all of us basically have a look at all sorts of online resources to see if any of them have some kind of intuitive biological profile that fits with the disease we’re thinking about.”

Of course, intuitive leads are not foolproof, nor are current mutation data-bases. (See sidebar, story end.) And so, MacArthur says, “we need to start replacing the sort of intuitive biological approach with a much more data-informed approach.”

Developing such an approach hinges in part on having more genomes. “If we get thousands — tens of thousands — of people sequenced with various different phenotypes that have been crisply identified, that’s going to be so important because it’s the coupling of the processing of the data with having rare variants, structural variants, all the other genomic variations to understand the relationship of whole-genome sequence of any particular phenotype and a sequence variant,” Scripps’ Topol says.

Vanderbilt’s Zhao says that sample size is still an issue. “Right now, the number of samples in each whole-genome sequencing-based publication is still very limited,” he says. At the same time, he adds, “when I read peers’ grant applications, they are proposing more and more whole-genome sequencing.”

When it comes to disease studies, sequencing a whole swath of apparently healthy people is not likely to ever be worthwhile. According to Utah’s Tavtigian, “the place where it is cost-effective is when you test cases and then, if something is found in the case, go on and test all of the first-degree relatives of the case — reflex testing for the first-degree relatives,” he says. “If there is something that’s pathogenic for heart disease or colon cancer or whatever is found in an index case, then there is a roughly 50 percent chance that the first-degree relatives are going to carry the same thing, whereas if you go and apply that same test to someone in the general population, the probability that they carry something of interest is a lot lower.”

But more genomes, even familial ones, are not the only missing elements. To fill in the functional blanks, researchers require multiple data types.

“We’ve been pretty much sequence-centric in our thinking for many years now because that was where are the attention [was],” Topol says. “But that leaves the other ‘omes out there.”

From the transcriptome to the proteome, the metabolome, the microbiome, and beyond — Topol says that because all the ‘omes contribute to human health, they all merit review.

“The ability to integrate information about the other ‘omics will probably be a critical direction to understand the underpinnings of disease,” he says. “I call it the ‘panoromic’ view — that is really going to become a critical future direction once we can do those other ‘omics readily. We’re quite a ways off from that right now.”

Mass General’s MacArthur envisages “rolling in data from protein-protein interaction networks and tissue expression data — pulling all of these together into a model that predicts, given the phenotype, given the systems that appear to be disrupted by this variant, what are the most likely set of genes to be involved,” he says. From there, whittling that set down to putative causal variants would be simpler.

“And at the end of that, I think we’ll end up with a relatively small number of variants, each of which has a probability score associated with it, along with a whole host of additional information that a clinician can just drill down into in an intuitive way in making a diagnosis in that individual,” he adds.

According to MacArthur, “we’re already moving in this direction — in five years I think we will have made substantial progress toward that.” He adds, “I certainly think within five years we will be diagnosing the majority of severe genetic disease patients; the vast majority of those we’ll be able to assign a likely causal variant using this type of approach.”

Tavtigian, however, highlights a potential pitfall. While he says that “integration of those [multivariate] data helps a lot with assessing unclassified variants,” it is not enough to help clinicians ascertain causality. Functional assays, which can be both inconclusive and costly, will be needed for some unclassified variant hits, particularly those that are thought to be clinically meaningful.

“I don’t see how you’re going to do a functional assay for less than like $1,000,” he says. “That means that unless the cost of the sequencing test also includes a whole bunch of money for assessing the unclassified variants, a sequencing test is going to create more of a mess than it cleans up.”

Rare, common

Despite the challenges, there have been plenty of clinical sequencing success stories. Already, Scripps’ Topol says there have been “two big fronts in 2012: One is the unknown diseases [and] the other one, of course, is cancer.” But scientists say that despite the challenges, whole–genome sequencing might also become clinically useful for asymptomatic individuals in the future.

Down the line, scientists have their sights set on sequencing asymptomatic individuals to predict disease risk. “The long-term goal is to have any person walk off the street, be able to take a look at their genome and, without even looking at them clinically, say: ‘This is a person who will almost certainly have phenotype X,'” MacArthur says. “That is a long way away. And, of course, there are many phenotypes that can’t be predicted from genetic data alone.”

Nearer term, Boston’s Kohane imagines that newborns might have their genomes screened for a number of neonatal or pediatric conditions.

Overall, he says, it’s tough to say exactly where all of the chips might fall. “It’s going to be an interesting few years where the sequencing companies will be aligning themselves with laboratory testing companies and with genome interpretation companies,” Kohane says.

Even if clinical sequencing does not show utility for cases other than genetic diseases, it could still become common practice.

“Worldwide, there are certainly millions of people with severe diseases that would benefit from whole–genome sequencing, so the demand is certainly there,” MacArthur says. “It’s just a question of whether we can develop the infrastructure that is required to turn the research-grade genomes that we’re generating at the moment into clinical-grade genomes. Given the demand and the practical benefit of having this information … I don’t think there is any question that we will continue to drive, pretty aggressively, towards large-scale -genome sequencing.”

Kohane adds that “although rare diseases are rare, in aggregate they’re actually not — 5 percent of the population, or 1 in 20, is beginning to look common.”

Despite conflicting reports as to its clinical value, given the rapid declines in cost, Kohane says it’s possible that a whole-genome sequence could be less expensive than a CT scan in the next five years. Confident that many of the interpretation issues will be worked out by then, he adds, “this soon-to-be-very-inexpensive test will actually have a lot of clinical value in a variety of situations. I think it will become part the decision procedure of most doctors.”


[Sidebar] ‘Predictive Capacity’ Challenged

In Science Translational Medicine in April, Johns Hopkins University School of Medicine’s Nicholas Roberts and his colleagues showed that personal genome sequences for healthy monozygotic twin pairs are not predictive of significant risk for 24 different diseases in those individuals and concluded that whole-genome sequencing was unlikely to be useful for that purpose.

As the Scripps Research Institute’s Eric Topol says, that Roberts and his colleagues examined the predictive capacity of personal genome sequencing “without any genome sequences” was but one flaw of their interpretation.

In a comment appearing in the same journal in May, Topol elaborated on this criticism, and noted that the Roberts et al. study essentially showed nothing new. “We cannot know the predictive capacity of whole-genome sequencing until we have sequenced a large number of individuals with like conditions,” Topol wrote.

Elsewhere in the journal, Tel Aviv University’s David Golan and Saharon Rosset noted that slightly tweaking the gene-environment parameters of the mathematical model used by Roberts et al. showed that the “predictive capacity of genomes may be higher than their maximal estimates.”

Colin Begg and Malcolm Pike from Memorial Sloan-Kettering Cancer Center also commented on the study in Science Translational Medicine, reporting their -alternative calculation of the predictive capacity of personal sequencing and their analysis of cancer occurrence in the second breast of breast cancer patients, both of which, they wrote, “offer a more optimistic view of the predictive value of genetic data.”

In response to those comments, Bert Vogelstein — who co-authored the Roberts et al. study — and his colleagues wrote in Science Translational Medicine that their “group was the first to show that unbiased genome-wide sequencing could illuminate the basis for a hereditary disease,” adding that they are “acutely aware of its immense power to elucidate disease pathogenesis.” However, Vogelstein and his colleagues also said that recognizing the potential limitations of personal genome sequencing is important to “minimize false expectations and foster the most fruitful investigations.”


[Sidebar] ‘The Single Biggest Problem’

That there is currently no comprehensive, accurate, and openly accessible database of human disease-causing mutations “is the single greatest failure of modern human genetics,” Massachusetts General Hospital’s Daniel MacArthur says.

“We’ve invested so much effort and so much money in researching these Mendelian diseases, and yet we have never managed as a community to centralize all of those mutations in a single resource that’s actually useful,” MacArthur says. While he notes that several groups have produced enormously helpful resources and that others are developing more, currently “none covers anywhere close to the whole of the literature with the degree of detail that is required to make an accurate interpretation.”

Because of this, he adds, researchers are pouring time and resources into rehashing one another’s efforts and chasing down false leads.

“As anyone at the moment who is sequencing genomes can tell you, when you look at a person’s genome and you compare it to any of these databases, you find things that just shouldn’t be there — homozygous mutations that are predicted to be severe, recessive, disease-causing variants and dominant mutations all over the place, maybe a dozen or more, that they’ve seen in every genome,” MacArthur says. “Those things are clearly not what they claim to be, in the sense that a person isn’t sick.” Most often, he adds, the researchers who reported that variant as disease-causing were mistaken. Less commonly, the database moderators are at fault.

“The single biggest problem is that the literature contains a lot of noise. There are things that have been reported to be mutations that just aren’t. And, of course, a lot of the databases are missing a lot of mutations as well,” MacArthur adds. “Until we have a complete database of severe disease mutations that we can trust, genome interpretation will always be far more complicated than it should be.”

Tracy Vence is a senior editor of Genome Technology.

Source: 

http://www.genomeweb.com/node/1098636/

NIST Consortium Embarks on Developing ‘Meter Stick of the Genome’ for Clinical Sequencing

September 05, 2012

The National Institute of Standards and Technology has founded a consortium, called “Genome in a Bottle,” to develop reference materials and performance metrics for clinical human genome sequencing.

Following an initial workshop in April, consortium members – which include stakeholders from industry, academia, and the government – met at NIST last month to discuss details and timelines for the project.

The current aim is to have the first reference genome — consisting of genomic DNA for a specific human sample and whole-genome sequencing data with variant calls for that sample — available by the end of next year, and another, more complete version by mid-2014.

“At present, there are no widely accepted genomics standards or quantitative performance metrics for confidence in variant calling,” the consortium wrote in its work plan, which was discussed at the meeting. Its main motivation is “to develop widely accepted reference materials and accompanying performance metrics to provide a strong scientific foundation for the development of regulations and professional standards for clinical sequencing.”

“This is like the meter stick of the genome,” said Marc Salit, leader of the Multiplexed Biomolecular Science group in NIST’s Materials Measurement Laboratory and one of the consortium’s organizers. He and his colleagues were approached by several vendors of next-generation sequencing instrumentation about the possibility of generating standards for assessing the performance of next-gen sequencing in clinical laboratories. The project, he said, will focus on whole-genome sequencing but will also include targeted sequencing applications.

The consortium, which receives funding from NIST and the Food and Drug Administration, is open for anyone to participate. About 100 people, representing 40 to 50 organizations, attended last month’s meeting, among them representatives from Illumina, Life Technologies, Pacific Biosciences, Complete Genomics, the FDA, the Centers for Disease Control and Prevention, commercial and academic clinical laboratories, and a number of large-scale sequencing centers.

Four working groups will be responsible for different aspects of the project: a group led by Andrew Grupe at Celera will select and design the reference materials; a group headed by Elliott Margulies at Illumina will characterize the reference materials experimentally, using multiple sequencing platforms; Steve Sherry at the National Center for Biotechnology Information is heading a bioinformatics, data integration, and data representation group to analyze and represent the experimental data; and Justin Johnson from EdgeBio is in charge of a performance metrics and “figures of merit” group to help laboratories use the reference materials to characterize their own performance.

The reference materials will include both human genomic DNA and synthetic DNA that can be used as spike-in controls. Eventually, NIST plans to release the references as Standard Reference Materials that will be “internationally recognized as certified reference materials of higher order.”

According to Salit, there was some discussion at the meeting about what sample to select for a national reference genome. The initial plan was to use a HapMap sample – NA12878, a female from the CEPH pedigree from Utah – but it turned out that HapMap samples are consented for research use only and not for commercial use, for example in an in vitro diagnostic or for potential re-identification from sequence data.

The genome of NA12878 has already been extensively characterized, and the CDC is developing it as a reference for clinical laboratories doing targeted sequencing. “We were going to build on that momentum and make our first reference material the same genome,” Salit said. But because of the consent issues, NIST’s institutional review board and legal experts are currently evaluating whether the sample can be used.

In the meantime, consortium members have been “quite enthusiastic” about using samples from the Harvard University’s Personal Genome Project, which are broadly consented, Salit said.

The reference material working group issued a recommendation to develop a set of genomes from eight ethnically diverse parent-child trios as references, he said. For cancer applications, the references may also potentially include a tumor-normal pair.

The consortium will characterize all reference materials by several sequencing platforms. Several instrument vendors, as well as a couple of academic labs, have offered to contribute to data production. According to Justin Zook, a biomedical engineer at NIST and another organizer of the consortium, the current plan is to use sequencing technology from Illumina, Life Technologies, Complete Genomics, and – at least for the first genome – PacBio. Some of the sequencing will be done internally at NIST, which has Life Tech’s 5500 and Ion Torrent PGM available. In addition, the consortium might consider fosmid sequencing, which would provide phasing information and lower the error rate, as well as optical mapping to gain structural information, Zook said.

He and his colleagues have developed new methods for calling consensus variants from different data sets already available for the NA12878 sample, which they are planning to submit for publication in the near future. A fraction of the genotype calls will be validated using other methods, such as microarrays and Sanger sequencing. Consensus genotypes with associated confidence levels will eventually be released publicly as NIST Reference Data.

An important part of NIST’s work on the data analysis will be to develop probabilistic confidence estimates for the variant calls. It will also be important to distinguish between homozygous reference genotypes and areas in the genome “where you’re not sure what the genotype is,” Zook said, adding that this will require new data formats.

Coming up with confidence estimates for the different types of variants will be challenging, Zook said, particularly for indels and structural variants. Also, representing complex variants has not been standardized yet.

Several meeting participants called for “reproducible research and transparency in the analysis,” Salit said, and there were discussions about how to implement that at the technical level, including data archives so anyone can re-analyze the reference data.

One of the challenges will be to establish the infrastructure for hosting the reference data, which will require help from the NCBI, Salit said. Also, analyzing the data collaboratively is “not a solved problem,” and the consortium is looking into cloud computing services for that.

The consortium will also develop methods that describe how to use the reference materials to assess the performance of a particular sequencing method, including both experimental protocols and open source software for comparing genotypes. “We could throw this over the fence and tell someone, ‘Here is the genome and here is the variant table,'” Salit said, but, he noted, the consortium would like to help clinical labs use those tools to understand their own performance.

Edge Bio’s Johnson, who is chairing the working group in charge of this effort, is also involved in developing bioinformatic tools to judge the quality of genomes for the Archon Genomics X Prize (CSN 11/2/2011). Salit said that NIST is “leveraging some excellent work coming out of the X Prize” and is collaborating with a member of the X Prize team on the consensus genotype calling project.

By the end of 2013, the consortium wants to have its first “genome in a bottle” and reference data with SNV and maybe indel calls available, which will not yet include all confidence estimates. Another version, to be released in mid-2014, will include further analysis of error rates and uncertainties, as well as additional types of variants, such as structural variation.

Julia Karow tracks trends in next-generation sequencing for research and clinical applications for GenomeWeb’s In Sequenceand Clinical Sequencing News. E-mail her here or follow her GenomeWeb Twitter accounts at @InSequence and@ClinSeqNews.
Source:

At AACC, NHGRI’s Green Lays out Vision for Genomic Medicine

July 16, 2012

LOS ANGELES – The age of genomic medicine is within “striking distance,” Eric Green, director of the National Human Genome Research Institute, told attendees of the American Association of Clinical Chemistry’s annual meeting here on Sunday.

Speaking at the conference’s opening plenary session, Green discussed NHGRI’sroadmap for moving genomic findings into clinical practice. While this so-called “helix to healthcare” vision may take many years to fully materialize, “I predict absolutely that it’s coming,” he said.

Green noted that rapid advances in DNA sequencing have put genomics on a similar development path as clinical chemistry, which is also a technology-driven field. “If you look over the history of clinical chemistry, whenever there were technology advances, it became incredibly powerful and new opportunities sprouted up left and right,” he said.

Green likened next-gen sequencing to the autoanalyzers that “changed the face of clinical chemistry” by providing a generic platform that enabled a range of applications. In a similar fashion, low-cost sequencing is becoming a “general purpose technology” that can not only read out DNA sequence but can also provide information about RNA, epigenetic modifications, and other associated biology, he said.

The “low-hanging fruit” for genomic medicine is cancer, where molecular profiling is already being used alongside traditional histopathology to provide information on prognosis and to help guide treatment, he said.

Another area where Green said that genomic medicine is already bearing fruit is pharmacogenomics, where genomic data is proving useful in determining which patients will respond to specific drugs.

Nevertheless, while it’s clear that “sequencing is already altering the clinical landscape,” Green urged caution. “We have to manage expectations and realize it’s going to be many years from going from the most basic information about our genome sequence to actually changing medical care in any serious way,” he said.

In particular, he noted that the clinical interpretation of genomic data is still a challenge. Not only are the data volumes formidable, but the functional role of most variants is still unknown, he noted.

This knowledge gap should be addressed over the next several years as NHGRI and other organizations worldwide sequence “hundreds of thousands” of human genomes as part of large-scale research studies.

“We’re increasingly thinking about how to use that data to actually do clinical care, but I want to emphasize that the great majority of this data being generated will and should be part of research studies and not part of primary clinical care quite yet,” Green said.

Source:

http://www.genomeweb.com/sequencing/aacc-nhgris-green-lays-out-vision-genomic-medicine

Startup Aims to Translate Hopkins Team’s Cancer Genomics Expertise into Patient Care

May 16, 2012

Researchers at Johns Hopkins University who helped pioneer cancer genome sequencing have launched a commercial effort intended to translate their experience into clinical care.

Personal Genome Diagnostics, founded in 2010 by Victor Velculescu and Luis Diaz, aims to commercialize a number of cancer genome analysis methods that have been developed at Hopkins over the past several decades. Velculescu, chief scientific officer of PGDx, is director of cancer genetics at the Ludwig Center for Cancer Genetics and Therapeutics at Hopkins; while Diaz, chief medical officer of the company, is director of translational medicine at the Ludwig Center.

Other founders include Ludwig Center Director Bert Vogelstein as well as Hopkins researchers Ken Kinzler, Nick Papadopoulos, and Shibin Zhou. The team has led a number of seminal cancer sequencing projects, including the first effort to apply large-scale sequencing to cancer genomes, one of the first cancer exome sequencingstudies, and the discovery of a number of cancer-related genes, including TP53, PIK3CA, APC, IDH1 and IDH2.

Velculescu told Clinical Sequencing News that the 10-person company, headquartered in the Science and Technology Park at Johns Hopkins in Baltimore, is a natural extension of the Hopkins group’s research activities.

Several years ago, “we began receiving requests from other researchers, other physicians, collaborators, and then actually patients, family members, and friends, wanting us to do these whole-exome analyses on cancer samples,” he said. “We realized that doing this in the laboratory wasn’t really the best place to do it, so for that reason we founded Personal Genome Diagnostics.”

The goal of the company, he said, “is to translate this history of our group’s experience of cancer genetics and our understanding of cancer biology, together with the technology that has now become available, and to ultimately perform these analyses for individual patients.”

The fledgling company has reached two commercial milestones in the last several weeks. First, it gained CLIA certification for cancer exome sequencing using the HiSeq 2000. In addition, it secured exclusive licensing rights from Hopkins for a technology called digital karyotyping, developed by Velculescu and colleagues to analyze copy number changes in cancer genomes.

PGDx offers a comprehensive cancer genome analysis service that combines exome sequencing with digital karyotyping, which isolates short sequence tags from specific genomic loci in order to identify chromosomal changes as well as amplifications and deletions.

The company sequences tumor-normal pairs and promises a turnaround time of six to 10 weeks, though Velculescu said that ongoing improvements in sequencing technology and the team’s analysis methods promise to reduce that time “significantly.” It is currently seeing turnaround times of under a month.

To date, the company has focused solely on the research market. Customers have included pharmaceutical and biotech companies, individual clinicians and researchers, and contract research organizations, while the scale of these projects has ranged from individual patients to thousands of exomes for clinical trials.

While the company performs its own sequencing for smaller projects, it relies on third-party service providers for larger studies.

PGDx specializes in all aspects of cancer genome analyses, but has a particular focus on the front and back end of the workflow, Velculescu said, including “library construction, pathologic review of the samples, dissection of tumor samples to enrich tumor purity, next generation sequencing, identification of tumor-specific alterations, and linking of these data to clinical and biologic information about human cancer.”

The sequencing step in the middle, however, “is really almost becoming a commodity,” he noted. “Although we’ve done it in house, we typically do outsource it and that allows us to scale with the size of these projects.”

He said that PGDx typically works with “a number of very high-quality sequence partners to do that part of it,” but he declined to disclose these partners.

On the front end, PGDx has developed “a variety of techniques that we’ve licensed and optimized from Hopkins that have allowed us to improve extraction of DNA from both frozen tissue and [formalin-fixed, paraffin-embedded] tissue, even at very small quantities,” Diaz said. The team has also developed methods “to maximize our ability to construct libraries, capture, and then perform exomic sequencing with digital karyotyping.”

Once the sequence data is in hand, “we have a pipeline that takes that information and deciphers the changes that are most likely to be related to the cancer and its genetic make-up,” he said. “That’s not trivial. It requires inspection by an experienced cancer geneticist.”

While the firm is working on automating the analysis, “it’s not something that is entirely automatable at this time and therefore cannot be commoditized,” Diaz said.

The firm issues a report for its customers that “provides information not only on the actual sequence changes which are of high quality, but what these changes are likely to do,” Velculescu said, including “information about diagnosis, prognosis, therapeutic targeting [information] or predictive information about the therapy, and clinical trials.”

So far, the company has relied primarily on word of mouth to raise awareness of its offerings. “We’ve literally been swamped with requests from people who just know us,” Velculescu said. “I think one of the major reasons people have been coming to us for either these small or very large contracts is that people are getting this type of NGS data and they don’t know what to do with it — whether it’s a researcher who doesn’t have a lot of experience in cancer or a clinician who hasn’t seen this type of data before.”

While there’s currently “a wealth in the ability to get data, there’s an inadequacy in being able to understand and interpret the data,” he said.

Pricing for the company’s services is on a case-by-case basis, but Diaz estimated that retail costs are currently between $5,000 and $10,000 per tumor-normal pair for research purposes. Clinical cases are more costly because the depth of coverage is deeper and additional analyses are required, as well as a physician interpretation.

A Cautious Approach

While the company’s ultimate goal is to help oncologists use genomic information to inform treatment for their patients, PGDx is “proceeding cautiously” in that direction, Diaz said.

The firm has so far sequenced around 50 tumor-normal pairs for individual patients, but these have been for “informational purposes,” he said, stressing that the company believes the field of cancer genomics is still in the “discovery” phase.

“I think we’re really at the beginning of the genomic revolution in cancer,” Diaz said. “We are partnering with pharma, with researchers, and with certain clinicians to start bringing this forward — not only as a discovery tool but eventually as a clinical application.”

“We do think that rushing into this right now is too soon, but we are building the infrastructure — for example our recent CLIA approval for cancer genome analyses — to do that,” he added.

This cautious approach sets the firm apart from some competitors, including Foundation Medicine, which is about to launch a targeted sequencing test that it is marketing as a diagnostic aid to help physicians tailor therapy for their patients. Diagnostic firm Asuragen is also offering cancer sequencing services based on a targeted approach (CSN 1/12/12), as are a number of academic labs.

Diaz said that PGDx’s comprehensive approach also sets it apart from these groups. “We think there’s a lot of clinically actionable information in the genome … and we don’t want to limit ourselves by just looking at a set of genes and saying that these may or may not have importance.”

While the genes in targeted panels “may have some data surrounding them with regard to prognosis, or in relation to a therapy, that’s really only a small part of the story when it comes to the patient’s cancer,” Diaz said.

“That’s why we would like to remain the company that looks at the entire cancer genome in a comprehensive fashion, because we don’t know enough yet to break it down to a few genes,” he said.

The company’s proprietary use of digital karyotyping to find copy number alterations is another differentiator, Velculescu said, because many cancer-associated genes — such as p16, EGFR, MYC, and HER2/neu — are only affected by copy number changes, not point mutations.

Ultimately, “we want to develop something that has value for the clinician,” Diaz said. “A clinician currently sees 20 to 30 patients a day and may have only a few minutes to look at a report. If [information from sequencing] doesn’t have immediate high-impact value, it’s going to be very hard to justify its use down the road.”

He added that the company is “thinking very hard about what we can squeeze out of the cancer genome to provide that high-impact clinical value — something that isn’t just going to improve the outcome of patients by a few months or weeks, but actually change the outlook of that patient substantially.”

Source:

http://www.genomeweb.com/sequencing/startup-aims-translate-hopkins-teams-cancer-genomics-expertise-patient-care

 
Bernadette Toner is editorial director for GenomeWeb’s premium content. E-mail her here or follow her GenomeWeb Twitter account at @GenomeWeb.

In Educational Symposium, Illumina to Sequence, Interpret Genomes of 50 Participants for $5K Each

June 27, 2012

This story was originally published June 25.

As part of a company-sponsored symposium this fall to “explore best practices for deploying next-generation sequencing in a clinical setting,” Illumina plans to sequence and analyze the genomes of around 50 participants for $5,000 each, Clinical Sequencing News has learned.

According to Matt Posard, senior vice president and general manager of Illumina’s translational and consumer genomics business, the event is part of a “multi-step process to engage experts in the field around whole-genome sequencing, and to support the conversation.”

The “Understand your Genome” symposium will take place Oct. 22-23 at Illumina’s headquarters in San Diego.

The company sent out invitations to the event over the last few months, targeting individuals with a professional interest in whole-genome sequencing, including medical geneticists, pathologists, academics, and industry or business leaders, Posard told CSN this week. To provide potential participants with more information about the symposium, Illumina also hosted a webinar this month that included a Q&A session.

Registration closed June 14 and has exceeded capacity — initially 50 spots, a number that may increase slightly, Posard said. Everyone else is currently waitlisted, and Illumina plans to host additional symposia next year.

“There has been quite a bit of unanticipated enthusiasm around this from people who are speaking at the event or planning to attend the event,” including postings on blogs and listservs, Posard said.

As part of their $5,000 registration fee, which does not include travel and lodging, participants will have their whole genome sequenced in Illumina’s CLIA-certified and CAP-accredited lab prior to the event. It is also possible to participate without having one’s genome sequenced, but only as a companion to a full registrant, according to Illumina’s website. The company prefers that participants submit their own sample, but as an alternative, they may submit a patient sample instead.

The general procedure is very similar to Illumina’s Individual Genome Sequencing, or IGS, service in that it requires a prescription from a physician, who also receives the results to review them with the participant. However, participants pay less than they would through IGS, where a single human genome currently costs $9,500.

Participants will also have a one-on-one session with an Illumina geneticist prior to being sequenced, and they can choose to not receive certain medical information as part of the genome interpretation.

Doctors will receive the results and review them with the participants sometime before the event. “There will be no surprises for these participants when they come to the symposium,” Posard said.

Results will include not only a list of variants but also a clinical interpretation of the data by Illumina geneticists. This is currently not part of IGS, which requires an interpretation of the data by a third party, but Illumina plans to start offering interpretation services for IGS before the symposium, Posard said.

“Our stated intent has always been that we want to fill in all of the pieces that the physicians require, so we are building a human resource, as well as an informatics team, to provide that clinical interpretation, and we are using that apparatus for the ‘Understand your Genome’ event,” Posard said.

The interpretation will include “a specified subset of genes relating to Mendelian conditions, drug response, and complex disease risks,” according to the website, which notes that “as with any clinical test, the patient and physician must discuss any medically significant results.”

The first day of the symposium will feature presentations on clinical, laboratory, ethical, legal, and social issues around whole-genome sequencing by experts in the field. Speakers include Eric Topol from the Scripps Translational Science Institute, Matthew Ferber from the Mayo Clinic, Robert Green from Brigham and Women’s Hospital and Harvard Medical School, Heidi Rehm from the Harvard Partners Center for Genetics and Genomics, Gregory Tsongalis from the Dartmouth Hitchcock Medical Center, Robert Best from the University of South Carolina School of Medicine, Kenneth Chahine from Ancestry.com, as well as Illumina’s CEO Jay Flatley and chief scientist David Bentley.

On the second day, participants will receive their genome data on an iPad and learn how to analyze their results using the iPad MyGenome application that Illumina launched in April.

The planned symposium stirred some controversy at the European Society of Human Genetics annual meeting in Nuremberg, Germany, this week. During a presentation in a session on the diagnostic use of next-generation sequencing, Gert Matthijs, head of the Laboratory for Molecular Diagnostics at the Center for Human Genetics in Leuven, Belgium, said he was upset because the invitation to Illumina’s event apparently not only reached selected individuals but also patient organizations.

“To me, personally, [the event] tells that some people are really exploring the limits of business, and business models, to get us to genome sequencing,” he said.

“We have to be very careful when we put next-generation sequencing direct to the consumer, or to patient testing, but it’s a free world,” he added later.

Posard said that Illumina welcomes questions about and criticism of the symposium. “This is another example of us being extremely responsible and transparent in how we’re handling this novel application that everybody acknowledges is the wave of the future,” he said. “We want to responsibly introduce that wave, and I believe we’re doing so, through such things as the ‘Understand your Genome’ event, but not limited to this event.”

Julia Karow tracks trends in next-generation sequencing for research and clinical applications for GenomeWeb’s In Sequenceand Clinical Sequencing News. E-mail her here or follow her GenomeWeb Twitter accounts at @InSequence and@ClinSeqNews.
Source:

Federal Court Rules Helicos Patent Invalid; Company Reaches Payment Agreement with Lenders

August 30, 2012

NEW YORK (GenomeWeb News) – A federal court has ruled in Illumina’s favor in a lawsuit filed by Helicos BioSciences that had alleged patent infringement.

In a decision dated Aug. 28, District Judge Sue Robinson of the US District Court for the District of Delaware granted Illumina’s motion for summary judgment declaring US Patent No 7,593,109 held by Helicos invalid for “lack of written description.”

Titled “Apparatus and methods for analyzing samples,” the patent relates to an apparatus, systems, and methods for biological sample analysis.

The ‘109 patent was the last of three patents that Helicos accused Illumina of infringing, following voluntary dismissal by Helicos earlier this year with prejudice of the other two patents. In October 2010 Helicos included Illumina and Life Technologies in a lawsuit that originally accused Pacific Biosciences of patent infringement.

Helicos dropped its lawsuit against Life Tech and settled with PacBio earlier this year, leaving Illumina as the sole defendant.

In seeking a motion for summary judgment, Illumina argued that the ‘109 patent does not disclose “a focusing light source operating with any one of the analytical light sources to focus said optical instrument on the sample.” Illumina’s expert witness further said that the patent “does not describe how focusing light source works” nor does it provide an illustration of such a system, according to court documents.

In handing down her decision, Robinson said, “In sum, and based on the record created by the parties, the court concludes that Illumina has demonstrated, by clear and convincing evidence, that the written description requirement has not been met.”

In a statement, Illumina President and CEO Jay Flatley said he was pleased with the court’s decision.

“The court’s ruling on the ‘109 patent, and Helicos’ voluntary dismissal of the other patents in the suit, vindicates our position that we do not infringe any valid Helicos patent,” he said. “While we respect valid and enforceable intellectual property rights of others, Illumina will continue to vigorously defend against unfounded claims of infringement.”

After the close of the market Wednesday, Helicos also disclosed that it had reached an agreement with lenders to waive defaults arising from Helicos’ failure to pay certain risk premium payments in connection with prior liquidity transactions. The transactions are part of risk premium payment agreement Helicos entered into with funds affiliated with Atlas Venture and Flagship Ventures in November 2010.

The lenders have agreed to defer the risk premium payments “until [10] business days after receipt of a written notice from the lenders demanding the payment of such risk premium payments,” Helicos said in a document filed with the US Securities and Exchange Commission.

The Cambridge, Mass.-based firm also disclosed that Noubar Afeyan and Peter Barrett have resigned from its board.

Helicos said two weeks ago that its second-quarter revenues dipped 29 percent year over year to $577,000. In an SEC document, it also warned that existing funds were not sufficient to support its operations and related litigation expenses through the planned September trial date for its dispute with Illumina.

In Thursday trade on the OTC market, shares of Helicos closed down 20 percent at $.04.

Source:

http://www.genomeweb.com/sequencing/federal-court-rules-helicos-patent-invalid-company-reaches-payment-agreement-len

State of the Science: Genomics and Cancer Research

April 2012
Basic research allows for a better understanding of cancer and, eventually, improved patient outcomes. Zhu Chen, China’s minister of health, and Shanghai Jiao Tong University’s Zhen-Yi Wang received the seventh annual Szent-Györgyi prize from the National Foundation for Cancer Research for their work on a treatment for acute promyelocytic leukemia. Genome Technology‘s Ciara Curtin spoke to Chen, Wang, and past prize winners about the state of cancer research.

Genome Technology: Doctors Wang and Chen, can you tell me a bit about the work you did that led to you receiving the Szent-Györgyi prize?

Zhen-Yi Wang: I am a physician. I am working in the clinic, so I have to serve the patients. … I know the genes very superficially, not very deeply, but the question raised to me is: There are so many genes, but how are [we] to judge what is the most important?

Zhu Chen: The work that is recognized by this year’s Szent-Györgyi Prize concerns … acute promyelocytic leukemia. Over the past few decades, we have been involved in developing new treatment strategies against this disease.

You have two [therapies — all-trans retinoic acid and arsenic trioxide] — that target the same protein but with slightly different mechanisms, so we call this synergistic targeting. When the two drugs combine together for the induction therapy, then we see very nice response in terms of the complete remission rate. But more importantly, we see that this synergistic targeting, together with the effect of the chemotherapy, can achieve a very high five-year disease-free survival — as high as 90 percent.

But we were more interested in the functional aspects of the genome, to understand what each gene does and also to particularly understand the network behavior of the genes.

GT: There are a number of consortiums looking at the genome sequences of many cancer types. What do you hope to see from such studies?

Webster Cavenee: This is a way that tumors are being sequenced in a rational kind of way. It would have been done anyway by labs individually, which would have taken a lot more money and taken a lot longer, too. The human genome sequence, everybody said, ‘Why are you going to do that?’ … But that now turns out to be a tremendous resource. … From the point of view of The Cancer Genome Atlas, having the catalog of all of the kinds of mutations which are present in tumors can be very useful because you can see patterns. For example, in the glioblastoma cancer genome project, they found an unexpected association of some mutations and combinations of mutations with drug sensitivity. Nobody would have thought that.

The problem, of course, is that when you are sequencing all these tumors, it’s a very static thing. You get one point in time and you sequence whatever comes out of this big lump of tissue. That big lump is made up of a lot of different kinds of pieces, so when you see a mutation, you can’t know where it came from and you don’t know whether it actually does anything. That then leads into what’s going to be the functionalizing of the genome. Because in the absence of knowing that it has a function, it’s not going to be of very much use to develop drugs or anything like that. And that’s a much bigger exercise because that involves a lot of experiments, not just stuffing stuff into a sequencer.Peter Vogt: [The genome] has to be used primarily to determine function. Without function, there’s not much you can do with these mutations, because the distinction between a driver mutation and a passenger mutation can’t be made just on the basis of sequence.

Carlo Croce: After that, you have to be able to validate all of the genetic operations in model systems where you can reproduce the same changes and see whether there are the same consequences. Otherwise, without validation, to develop therapy doesn’t make much sense because maybe those so-called driver mutations will turn out to be something else.

GT: Will sequencing of patient’s tumors come to the clinic?

CC: It is inevitable. Naturally, there are a lot of bottlenecks. To do the sequencing is the, quote, trivial part and it is going to cost less and less. But then interpreting the data might be a little bit more cumbersome.

Sujuan Ba: Dr. Chen, there is an e-health card in China right now. Do you think some day gene sequencing will be stored in that card?

ZC: We are developing a digital healthcare in China. We started with electronic health records and now by providing the e-health card to the people, that will facilitate the individualized health management and also the supervision of our healthcare system. In terms of the use of genetic information for clinical purposes, as Professor Croce said, it’s going to happen.

GT: What do you think are the major questions in cancer research that still need to be addressed?

PV: There are increasingly two schools of thought on cancer. One is that it is all an engineering problem: We have all the information we need, we just need to engineer the right drugs. The other school says it’s still a basic knowledge problem. I think more and more people think it’s just an engineering problem — give us the money and we’ll do it all. A lot of things can be done, but we still don’t have complete knowledge.

Roundtable Participants
Sujuan Ba, National Foundation for Cancer Research
Webster Cavenee, University of California, San Diego
Zhu Chen, Ministry of Health, China
Carlo Croce, Ohio State University
Peter Vogt, Scripps Research Institute
Zhen-Yi Wang, Shanghai Jiao Tong University

Source:

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Reporter: Aviva Lev-Ari, PhD, RN

Game On

September 2012

Combining gaming and genomics may sound odd, but play can produce useful data. By presenting complex biological problems as games and distributing those games far and wide, researchers can take advantage of a large network of virtual computation in the form of thousands of players. Games can also harness the natural human ability for pattern recognition and take advantage of the ways in which the human brain is better at that than even the most powerful supercomputer.

One of the first games to harness the power of the crowd was Foldit, which was developed by the University of Washington’s David Baker in 2008. Foldit encourages players to solve protein structure prediction problems by folding proteins into stable shapes.

Last September, an elite contingent of 15 Foldit players used molecular replacement to solve the crystal structure of a retroviral protease from the Mason-Pfizer Monkey Virus, which causes simian AIDS.

Baker’s team published a paper in Nature Structural & Molecular Biology describing how the solutions facilitated the identification of novel structural features that could provide a foundation for the design of new antiretroviral drugs. According to the authors, this marked the first time gamers solved a longstanding -biological problem.

Then in December 2010, a team from McGill University rolled out Phylo, a Sudoku-like game that utilizes players’ abilities to match visual patterns between regions of similarity in multiple sequence alignments. Phylo’s designers reported in a PLOS One paper published in March that, since the game’s launch, they had received more than 350,000 solutions produced by more than 12,000 registered players.

“We don’t know right now what other interesting problems we could solve using these crowdsourcing techniques. We still have a lack of deep understanding about when human intuition or help is very useful,” says Jérôme Waldispühl, an assistant professor at McGill University and lead developer of Phylo. “But what I like is the involvement of society digging into the most meaningful and deep scientific questions — you are trying to involve society into the very process of scientific discovery.”

Last year, a group from Carnegie Mellon University and Stanford University released an online game called EteRNA, the purpose of which is to help investigators envision RNA knots, polyhedra, and any other RNA shapes that have yet to be identified. Top designs are analyzed each week to determine if the molecules can fold themselves into the 3D shapes predicted by RNA modeling software.

Purposeful play

More “games with a purpose” — as they are sometimes called — aimed at solving biological problems are in development.

“No matter how big your super-computer is, you can’t try all gene combinations within a 20,000-gene space,” says Benjamin Good, a research associate at the Scripps Research Institute. “Humans have a role to play here because maybe we can do better than what happens when you just compute for just many, many random datasets.”

Good and his colleagues have developed a suite of games, called Gene Games, which they hope to use to build out genomic databases and to improve existing algorithms. This suite includes GenESP, a two-player game in which both players see the same disease and each must guess what gene the other is typing from a dropdown list of possible genes. This game is aimed at an audience with some knowledge of the field and takes advantage of players’ expertise.

Another game is Combo, which challenges players to find the ideal combination of genes for phenotype prediction. Combo players can choose to start at an introductory level where they separate mammals from other animals or divide the animal kingdom into five classes, or begin at a more challenging level where they have to identify gene expression signatures in tumors to predict survival or metastasis.

“The goal of issuing GenESP is to provide a new way of building out gene annotation databases, and Combo is specifically made to enrich a machine-learning algorithm. It’s all an attempt to use games to tap into a large communities of people to get after what they know,” Good says.

But he is quick to point out that there is no specific critical mass of players that will provide the desired data — instead, it is about finding the right players just as the Foldit project seems to have done.

“I can’t say when we hit 1,000 users or 10,000 users, we’ll have X units of compute available to us — it just doesn’t work like that. But if we end up getting the right 100 people playing these games, we can make a lot of progress,” Good adds.

Diagnostic disport

Whether taking a crowdsourcing approach to access networks of thousands of players or to get at a handful of skilled players, gaming can not only provide new data for researchers, but can also provide a handy diagnostic resource for clinicians.

In May, a group from the University of California, Los Angeles, released Molt, a game in which players aid in the diagnosis of malaria-infected red blood cells. After completing training, players are presented with frames of red blood cell images and use a virtual syringe tool to eliminate infected cells and then use a collect-all tool to designate the remaining cells in the frame as healthy. Results from the games are sent back to the point-of-care or hospital setting.

Popular online games are also providing models for new bioinformatics applications. A new software tool called ImageJS marries bioinformatics with pathology, which its developers say takes its cue from Rovio Entertainment’s popular Angry Birds game. Developed by a team at the University of Alabama at Birmingham, this free app allows pathologists to drag pathology slides into a Web app to identify malignancies based on color.

“There are two bioinformatics problems at the point of care that an Angry Birds-approach would solve. The first is that it delivers the code to the machine rather than forcing the data to travel, so the code does the traveling,” says Jonas Almeida, a professor at UAB. “The second problem it solves is that it doesn’t require installation of any application; they are written in JavaScript, which is a native language of Web development, and the application has no access to the local file system, so we have an application that does not make the IT people nervous.”

Almeida and his team have also designed a module for ImageJS that can analyze genomes using the same visual interface as the malignancy–diagnosis module to provide clinicians with even better diagnostic accuracy. In the spirit of crowdsourcing, Almeida adds that the success of ImageJS will rely upon the willingness of its users to develop their own modules to solve their own specific problems using the game-like interface.

“Funding agencies are also interested in these out-of-the-box solutions. However, there is also some skepticism that will probably need more time to be overcome through clear success stories with these new gaming based solutions to existing problems,” says Molt’s designer Aydogan Ozcan, an associate professor at UCLA.

Despite the funding limitations — and the formidable challenge of designing a game that people will want to play — gaming is gaining traction and enjoying a favorable reception from the research community.

“On a one-to-one basis, everyone seems to love it. They get the potential and are just waiting to see what is going to happen,” Scripps’ Good says. “But developing these games is an enormous challenge. Our background is in bioinformatics, it’s not in making things that are fun. It’s hard to make a fun game all by itself, let alone make one that will solve a difficult problem.”

Matthew Dublin is a senior writer at Genome Technology.

http://www.genomeweb.com//node/1122001?hq_e=el&hq_m=1336360&hq_l=3&hq_v=e1df6f3681

 

Related topic on this Scientific Web Site

‘Gamifying’ Drug R&D: Boehringer Ingelheim, Sanofi, Eli Lilly

http://pharmaceuticalintelligence.com/2012/08/22/gamifying-drug-rd-boehringer-ingelheim-sanofi-eli-lilly/

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Reporter and Curator: Dr. Sudipta Saha, Ph.D.

Targeting a protein important for chromatin organization could be a new strategy for male birth control. Proper regulation of chromatin dynamics is critical for proper sperm development, and mice with alterations in a protein that is central to chromatin organization are infertile. Now, scientists show that treating mice with a drug known to inhibit that protein impedes sperm development and renders the animals infertile—but halting treatment allows sperm production to restart and mice to sire normal litters.

The results, published in Cell, suggest that targeting this protein could produce a safe, reversible method for non-hormonal male contraception—a long-sought goal that has so far failed to materialize as an option alongside condoms and vasectomies.

Hormonal male contraception methods are already well-established. Male hormonal contraception works at least as well as a typical female oral contraceptive pill. But such contraceptives still have some significant hurdles to overcome before making it to market.

First, the strategy, which involves administering a hormone (usually a progestin) to halt production of testosterone and thus inhibit sperm development, does not suppress sperm production enough in every man. It also requires dosing with enough exogenous testosterone to maintain libido and muscle mass, but there’s currently no cheap and easily applied testosterone on the market. Furthermore, hormone-based male contraception can cause side effects. Unlike side effects for the female hormonal contraception, these can’t be balanced against the risks of pregnancy, which are often higher, noted John Amory at the University of Washington. Because men don’t run the same medical risks of pregnancy, there’s a higher bar for ensuring that contraception administered to healthy men doesn’t carry risks. Finally, despite worldwide surveys suggesting public receptiveness to a male contraceptive pill, pharmaceutical companies no longer fund development of such drugs.

Some of these issues have spurred researchers to look for a non-hormonal way to temporarily induce infertility in men, which should cause with fewer side effects and be more appealing to pharma. Amory’s work, for example, has shown that a compound that targets the retinoic acid pathway of sperm development reversibly inhibits sperm production. The drug’s potential is hamstrung by the fact that men taking the drug can’t consume alcohol without nausea—a side effect he’s currently working to circumvent.

The current study builds on previous work by Debra Wolgemuth at Columbia University showing that BRDT—a testes-specific member of a family of bromodomain-containing proteins, which are important for regulating chromatin organization in various tissues—was critical for normal sperm development in mice. Truncating BRDT has an amazing effect on haploid sperm development. Removing the first bromodomain results in production of a shortened protein and, consequently, the aberrant organization and packaging of DNA in the sperm cells produced. Spermatids fail to elongate normally in mutant mice, resulting in decreased sperm production, misshapen sperm, and infertility.

In order to test the possibility that a BRDT-inhibiting drug, JQ1, might have potential as a male contraceptive, Martin Matzuk of Baylor College of Medicine and his collaborators injected male mice daily with the drug, and examined their testis volume. This volume, which reflects the amount of sperm in the testes, dropped by 60 percent over the 6 weeks of treatment. The sperm count of these mice was nearly 90 percent lower than in control mice, and sperm motility also plunged in JQ1-treated mice, collectively resulting in infertility. Though JQ1 is known to inhibit related proteins expressed elsewhere in the body, the mice seemed to have no other effects from JQ1 treatment, and normal hormone levels in treated mice suggested that infertility wasn’t the result of a hormone imbalance.

A closer look at sperm generation in JQ1-treated mice suggested that sperm development was primarily blocked after the sperm cells had undergone meiosis, but before they began the process of elongating—a similar stage to that seen in BRDT-mutant mice. Importantly, the mice regained the ability to sire pups after several weeks off the drug.

The reversibility of the treatment is likely attributable to the fact that the researchers are targeting sperm cells midway through development, rather than accessory cells that support sperm development from stem cells, noted Michael Griswold, who studies sperm cell development at Washington State University, but did not participate in the study. It’s “a great place to inhibit, because you don’t get sperm cells, but you don’t affect stem cells, which makes [the treatment] reversible,” he explained.

Whether JQ1 acts by primarily targeting BRDT and derailing chromatin organization or whether it inhibits other family members expressed during sperm development remains unclear. Matzuk and his colleagues examined gene expression in JQ1-treated and control mice, and saw decreased expression of many genes important for meiosis, suggesting that JQ1 may be working by affecting transcription of a suite of important genes for spermatogensis. Also, because JQ1 also inhibits BRDT-related proteins, researchers need to be watchful for long-term side effects not detected in the current study, Matzuk noted. Going forward, it will be important to design drugs that selectively target BDRT.

Source References:

 

http://www.ncbi.nlm.nih.gov/pubmed?term=Small-molecule%20inhibition%20of%20BRDT%20for%20male%20contraception

http://the-scientist.com/2012/08/16/hope-for-male-contraception/?goback=%2Egde_3695897_member_148573151

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Reporter: Aviva Lev-Ari, PhD, RN
Blood. 2012 Aug 24. [Epub ahead of print]

Chromatin accessibility, p300 and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia.

Source

Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, Netherlands;

Abstract

Chromatin accessibility plays a key role in regulating cell type specific gene expression during hematopoiesis, but has also been suggested to be aberrantly regulated during leukemogenesis. To understand the leukemogenic chromatin signature we analyzed acute promyelocytic leukemia (APL), a subtype of leukemia characterized by the expression of RARα-fusion proteins such as PML-RARα. We used nuclease accessibility sequencing in cell lines as well as patient blasts to identify accessible DNA elements and identified over 100,000 accessible regions in each case. Using ChIP-seq we identified H2A.Z as a histone modification generally associated with these accessible regions while unsupervised clustering analysis of other chromatin features including DNA methylation, H2A.Zac, H3ac, H3K9me3, H3K27me3 and the regulatory factor p300 distinguished six distinct clusters of accessible sites, each with a characteristic functional make-up. Of these, PML-RARα binding was found specifically at accessible chromatin regions characterized by p300 binding and hypoacetylated histones. Identifying regions with a similar epigenetic make up in t(8;21) AML cells, another subtype of AMLs, revealed that these regions are occupied by the oncofusion protein AML1-ETO. Together our results suggest that oncofusion proteins localize to accessible regions and that chromatin accessibility together with p300 binding and histone acetylation characterize AML1-ETO and PML-RARα binding sites.

 

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Author and Curator: Chloe Thomas, Manager, Scientific Sessions and Education at Heart Rhythm Society

 

One step further towards an HIV vaccine

Statistics show that approximately 34 million people are infected with the Human Immunodeficiency Virus. Within the last years, important steps have been taken in finding treatments and medications against HIV. The study introduced in this article is a helpful contribution to the development of an HIV vaccine.

Cloning antibodies

Researchers working in the California Institute of Technology have focused more closely on the binding mechanism of the virus to the human cell. Leading a study which was published in the Science Magazine in 2011, they departed from the fact that a passive transfer of HIV neutralizing antibodies can prevent an infection and might therefore even be valuable for the creation of an HIV vaccine. As the number of naturally occurring antibodies is relatively low, the researchers intended to discover whether these antibodies belong to a larger group of molecules which might turn out useful studies of the infection. By cloning more than 500 HIV antibodies taken from four different infected individuals, they discovered that all of them produced a large number of potent HIV antibodies which mimic the binding to CD4. By isolating the potent anti-HIV antibodies of infected people, the scientists have begun to develop ways in order to neutralize subtypes of the infection. The researchers have found a strong version of an anti-HIV antibody, which is named NIH45-46. These antibodies that target the binding site of the host receptor (namely CD4) interact with the protein gp120. This protein sits on the viruses and helps the virus enter the cell, and thus mainly contributes to the infection process. The interaction between antibody and the protein leads to neutralizing the virus and thus may avoid infection. Knowing this, the scientists were able to develop an even stronger type, named NIH45-46G54W, which employs the described mechanism more effectively. The next step the researchers are advocating is a clinical testing period for the newly-created effective antibody. Through that, they hope to gain further information on understanding the neutralization of the virus which might even help in developing a vaccine against HIV.

Scientific research: a long process

Despite the success of the study, it is important to note that an analysis in the laboratories and a clinical testing phase has to be conducted over a long period of time in order to bring about representative results. Methods have to be considered, antibodies suppliers like here have to be contacted, and data have to be evaluated. For that reason, the development of an HIV vaccine cannot happen overnight, but should be furthered patiently.

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Cardiovascular Outcomes: Function of circulating Endothelial Progenitor Cells (cEPCs): Exploring Pharmaco-therapy targeted at Endogenous Augmentation of cEPCs

Author and Curator: Aviva Lev-Ari, PhD, RN

UPDATED on 1/25/2018

The secret to building a strong heart lies in blood vessels, Stanford researcher find

Curiously, blood flow through those missing vessels – and the oxygen it provides – is only part of the story. In a follow-up experiment, the researchers grew heart muscles in a dish along with endothelial cells that had not yet formed into blood vessels. The team found that when those endothelial cells produced no Ino80, the heart muscle didn’t develop properly. Apparently, Red-Horse said, “endothelial cells are producing something that’s a growth factor” for cardiac muscle cells. “The next step is to identify that factor.”

https://news.stanford.edu/2018/01/25/secret-building-strong-heart-blood-vessels/

This is a post in Clinical Cardiology Frontiers:

  • Resident-Cell-based Therapy and
  • Molecular Cardiology

An Overview of the State of  Science on Circulating Endothelial Progenitor Cells (cEPCs) and Cardiovascular Outcomes: Exploring Pharmaco-therapy targeted at Endogenous augmentation of cEPCs

 

Werner (2005) reported that after 12 months a total of 43 participants died, 23 from cardiovascular(CV) causes. A first major cardiovascular event occurred in 214 patients in 519 patients with coronary artery disease as confirmed on angiography. Endothelial progenitor cells (EPCs) derived from bone marrow are believed to support the integrity of the vascular endothelium. His study identified that the number and function of endothelial progenitor cells correlate inversely with cardiovascular risk factors, but the prognostic value associated with circulating endothelial progenitor cells has not been defined. The level of circulating CD34+KDR+endothelial progenitor cells predicts the occurrence of cardiovascular events and death from cardiovascular causes and may help to identify patients at increased cardiovascular risk. The number of endothelial progenitor cells positive for CD34 and kinase insert domain receptor (KDR) was determined with the use of flow cytometry, they evaluated the association between baseline levels of endothelial progenitor cells and death from cardiovascular causes, the occurrence of a first major cardiovascular event (myocardial infarction, hospitalization, revascularization, or death from cardiovascular causes), revascularization, hospitalization, and death from all causes (italics added).

Werner (2005) reported that after 12 months a total of 43 participants died, 23 from cardiovascular(CV) causes. A first major cardiovascular event occurred in 214 patients in 519 patients with coronary artery disease as confirmed on angiography. Endothelial progenitor cells (EPCs) derived from bone marrow are believed to support the integrity of the vascular endothelium. His study identified that the number and function of endothelial progenitor cells correlate inversely with cardiovascular risk factors, but the prognostic value associated with circulating endothelial progenitor cells has not been defined. The level of circulating CD34+KDR+endothelial progenitor cells predicts the occurrence of cardiovascular events and death from cardiovascular causes and may help to identify patients at increased cardiovascular risk. The number of endothelial progenitor cells positive for CD34 and kinase insert domain receptor (KDR) was determined with the use of flow cytometry, they evaluated the association between baseline levels of endothelial progenitor cells and death from cardiovascular causes, the occurrence of a first major cardiovascular event (myocardial infarction, hospitalization, revascularization, or death from cardiovascular causes), revascularization, hospitalization, and death from all causes (italics added).

In light of the inverse correlation found between CV risk and enumeration and function of cEPCs, this study proposes a pharmaco-therapeutic method to enhance the cell count by a method of endogenous augmentation as presented in Part II and called ElectEagle.

 

Phenotypic Identification of Circulating Endothelial Progenitor Cells (cEPCs)

 

In the current state of science on cEPCs, the definition of these cells is ambiguous, as found in Fadini et al. (2004) letter to the Editors of Heart. On this subject, additional five letters were addressed to NEJM Editor in 2005, in reference to Werner et al. (2005) article Correspondence titled: Circulation Endothelial Progenitor Cells. Werner et al. (2005) was in fact the stimulant for this project which takes his result as a starting point and carries the research into pharmaco-therapy and device design for diagnostic based on a quantitative model derived from Werner’s data.

In the article in Heart, peripheral blood CD34+ cells are defined as endothelial progenitor cells. In Fadini’s concern he notes that cEPCs represent a subset of peripheral blood mononuclear cells (PBMNCs) expressing immature surface markers common to hematopoietic stem cells and endothelial lineage markers. By contrast CD34 represents a marker of immature staminal cells that may be used to characterize EPCs together with other surface antigens, but that identifies not only EPCs. Peripheral blood CD34+ cells form a very heterogeneous pool containing also CD45+ cells (lymphatic precursors), CD14+ cells (monocyte/macrophage lineage precursors) and other non-hematopoietic cells not belonging to the endothelial lineage.

Fadini’s concern is supported by George et al. (2006), who concluded that current methods for quantitatively assessing numbers of circulating EPC are not correlated. George’s findings may suggest that CD34/KDR is more appropriate for the definition of circulating EPC, whereas CFU (colony forming Unit) numbers are more likely to reflect their ability to proliferate. Fadini’s research supports the percentage of EPCs among the CD34+ pool vary widely from patient to patient and, in the same patient, under different pathophysiological conditions, indicating possible peripheral differentiation rather than bone-marrow mobilization. His observation is supported by Lapidot & Petit (2002) and Hur et al., (2004).

Furthermore, CD133 is considered the best surface marker to define, identify and isolate circulating EPCs. Even if the exact phenotype of EPCs has not been clearly established, additional markers reflecting endothelial commitment, including Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2 or KDR), Platelet-Endothelial Cells Adhesion Molecule-1 (PECAM-1 or CD31), Vascular Endothelial-Cadherin, von Willebrand Factor, c-kit, Tie-2 and VEGFR-1, are required. Using flow cytometry less than 0,001% of PBMNCs is identified as EPCs, but two or three markers are needed to avoid unspecific count. Thus minimal requirement to identify EPCs should be the parallel use of CD34 (or CD133) and KDR expression, as supported by George (2006).

Thus, he suggests that PBMNCs-derived CD34+ cells may not be used to identify EPCs. Fadini suggests that if we consider that EPCs or CD34+ cells stimulate angiogenesis in a paracrine way by means of producing growth factors, then, it would be more appropriate to call them “Circulating Angiogenic Cells” (CACs) as already proposed. EPCs reduction and endothelial dysfunction as observed by circulating cells and vascular wall cells of diabetic patients are exposed to high oxidative stress, thus increased apoptosis or reduced peripheral differentiation are likely to explain low EPCs counts. Several other clinical conditions characterized by poor endothelial function, like diabetes mellitus, obesity, hypertension, autoimmune disorders (such as Systemic Lupus Erythematosus), chronic renal diseases, etc., all are likely to be influenced by EPCs reduction (Fadini, 2004).

The five letters to NEJM Editor, Kim et al (2005) are of great scientific merit and of great interest to this project. We are developing new intellectual property (IP) in several forms in Part II and Part III. The IP in Part III is actually using Werner et al. (2005a) data, for our method called ElectEagle. Therefore, here, Werner’s (2005b) points will be considered as his reply to the five letter correspondence and no discussion of the content of the five letters is presented.

  •           Werner & Nickenig (2005b) disagree with Bertolini et al. that CD34+KDR+ cells are mature circulating endothelial cells. Endothelial cells are predominantly identified by the presence of CD146 (and results of Boos et al., as described in their letter).
  •           In Werner et al (2005a), CD146+ circulating endothelial cells were not predictive of cardiovascular outcomes, which indicates that CD34+KDR+ cells differ substantially from circulating endothelial cells (unpublished data). It is an accepted standard to identify circulating endothelial progenitor cells by the presence of CD34 and KDR.
  •           To confirm the results, Werner et al (2005a) measured CD133+ endothelial progenitor cells and obtained similar results, which appear in the online Supplementary Appendix to our article.
  •           Drs. Ott and Taylor suggest calculating the absolute number of endothelial progenitor cells with the use of peripheral-blood mononuclear cells or lymphocytes. However, absolute cell counts measured by flow cytometry can be determined only with the use of enumeration systems (e.g., flow count beads).
  •           At present, we cannot think of a major advantage to measuring the absolute number of endothelial progenitor cells. The method provided allows a single measurement that is easy to perform, highly predictive, and transferable to other laboratories.
  •           Dr. Kim and Dr. Leu and colleagues address  the role of endothelial progenitor cells in acute coronary syndromes and acute myocardial infarction. Only one study has investigated the mobilization of CD34+KDR+ endothelial progenitor cells in myocardial infarction, whereas other studies have measured CD34+ cells or non–endothelial progenitor cell subfractions.
  •           None of the studies have systematically looked at the time course directly after acute myocardial infarction, owing to the fact that the exact onset of myocardial infarction is difficult to determine. Treatment of myocardial infarction requires the administration of multiple drugs that may influence the number of endothelial progenitor cells. Therefore, current data on progenitor cells in myocardial infarction are questionable.
  •           In order to elucidate the mobilization of endothelial progenitor cells after myocardial infarction, Werner et al (2005a) measured the number of CD34+KDR+ cells in patients undergoing transcoronary ablation of septal hypertrophy (unpublished data). Preliminary results indicate that directly after myocardial infarction, the number of endothelial progenitor cells decreases as a result of consumption of cells within the ischemic region. The increase in cells described previously may be due to medical treatment.
  •           No patient who was included in the study had had a recent ischemic event, so misclassification of patients was not an issue.
  •           Werner et al. (2005a) did not find an association between high sensitivity CRP measures and the number of endothelial progenitor cells. To their knowledge, there are no data available on the association between endothelial progenitor cells and inflammatory markers in a similar population of patients. Data that are available come from in vitro, animal, and small-scale studies investigating the role of endothelial progenitor cells in acute coronary syndromes. Since their study population consisted mainly of patients with stable coronary artery disease, this may explain the lack of an association.

Circulating Endothelial Cells (cECs) and Circulating Endothelial Progenitor Cells (cEPCs)

Vascular endothelial cells (EC) respond to numerous pathophysiological stimuli such as growth factors, cytokines, lipoproteins, and oxidative stress. Prolonged or unregulated activation of these cells often results in a loss of EC integrity and, thus, dysfunction—a process that can be assessed by the use of specific plasma markers such as von Willebrand factor (vWf), tissue plasminogen activator, soluble EC protein C receptor, soluble E selectin, and soluble thrombomodulin, as well as physiological techniques such as flow-mediated dilatation (FMD). Indeed, endothelial perturbation in cancer may well contribute to an increased risk of thrombosis in these patients. (Goon et al., 2006)

The presence of circulating endothelial cells (cECs) has recently been recognized as a useful marker of vascular damage. Usually absent in the blood of healthy individuals, cECs counts are elevated in diseases hallmarked by the presence of vascular insult, such as sickle cell anemia, acute myocardial infarction, Cytomegalovirus (CMV) infection, endotoxemia, and neoplastic processes. Current opinion suggests toxemia, that cECs are cells driven from the intima after vascular insult, and are thus the consequence—rather than the initiator—of a particular pathology (Goon et al., 2006).

A related circulating cell population are endothelial progenitor cells (cEPCs), which originate from the bone marrow, rather than from vessel walls. Seen in small numbers in healthy individuals, their numbers tend to increase following vascular injury. So far, experiments have established the ability of EPCs to form colonies in vitro, suggesting a role in both angio-genesis and in the, maintenance of existing vessel walls.

CEC are generally accepted as cells expressing endothelial markers [e.g., vWf, CD146, and vascular endothelial cadherin (VE-cadherin)] in the absence of hematopoietic (CD45 and CD14) and progenitor (CD133) markers. Interestingly, the progenitor marker CD34 is also present on mature cECs. Although CD146 is widely regarded as the principal marker for cECs (mature cell form), it has also been described in trophoblasts, mesenchymal stem cells, periodontal and malignant (prostatic cancer and melanoma) tissues, and activated lymphocytes (Goon et al., 2006).

Optimal Method for cECs and cEPCs Quantification (Cell Count) Remains Unknown

Together with EPCs, cECs only represent between 0.01% and 0.0001% of mononuclear cells in normal peripheral blood (Khan et al. (2005), making it very difficult to accurately quantify their numbers. To do this, it is often necessary to employ cell enrichment techniques combined with specific cell marker labeling.  The immunobead capture method (immunomagnetic beads bearing CD146 antibodies) developed by George et al. (1992) is the most widely used. Immunobeads have been successfully employed by other investigators, albeit with modifications [e.g., addition of EDTA and albumin to minimize cECs autoaggregation; drying cECs on a glass slide before counting (this enables storage at room temperature and secondary labeling); use of UEA-1 (an EC-specific stain); addition of an Fc receptor blocking agent, and double labeling for further analyses (e.g., for CD31 and CD34)]. After cell separation, either fluorescence microscopy, immunocyto-chemistry, or flow cytometry is used to confirm the endothelial chemistry, phenotype of the cells. Other methods used to concentrate mononuclear cell suspensions include standard and density (Lymphoprep, Axis-Shield, Oslo, Norway; Percoll, Sigma, St. Louis, MO; Ficoll, Sigma) centrifugation and mononuclear cell culturing on fibronectin-coated plates. The main alter- alternative to the immunobead method is flow cytometry” (Goon, 2006).

Werner et al. (2005a) used the following method for Flow Cytometry — For fluorescence-activated cell-sorting analysis, mononuclear cells were resuspended in 100 µl of a fluorescence-activated cell-sorting buffer containing phosphate-buffered saline, 0.1 percent bovine albumin, and aprotinin (20 µl per milliliter). Immunofluorescent cell staining was performed with the use of the fluorescent conjugated antibody CD34–fluorescein isothiocyanate (FITC) (10 µl; Becton Dickinson), KDR (kinase insert domain receptor), and CD133–phycoerythrin (PE) (10 µl; Miltenyi). For the identification of KDR+ cells, indirect immunolabeling was performed with the use of a biotinylated goat mononuclear antibody against the extracellular domain of human KDR (R&D Systems). IgG2a–FITC–PE antibody (Becton Dickinson) served as a negative control. For staining of KDR, extensive blocking was required with the use of human immunoglobulin (polyglobulin, 10 percent; Bayer) and goat serum (Sigma-Aldrich). Cell fluorescence was measured immediately after staining, and data were analyzed with the use of CellQuest software (FACS Calibur, Becton Dickinson). Units of all measured components are absolute cell counts obtained after the measurement of 10,000 events in the lymphocyte gate. To assess the reproducibility of the measurements, two separate blood samples were obtained, on days 0 and 7, from 10 subjects. The intraclass correlation between the two probes was 0.94. Probes were measured at the same time of day, with identical instrument settings, by two investigators. For each patient, a corresponding negative control with IgG2a–FITC–PE antibody was obtained.

Colony-Forming Units of Endothelial Cells (Werner et al. 2005a)

In an endothelial basal medium (CellSystems) with supplements, 1×107 mononuclear cells were seeded on human fibronectin–coated plates (Sigma-Aldrich). After 48 hours, 1×106 nonadherent cells were transferred into new fibronectin-coated wells to avoid contamination with mature endothelial cells and nonprogenitor cells.22 After seven days in vitro, endothelial colony-forming units in at least three wells were counted by two independent investigators. Colony-forming units of endothelial cells are expressed as absolute numbers of colonies per well. (Werner, et al. 2005)

George et al. (2006) reports using the following method while performing an analysis of several methods used for cEPCs assessment and correlated them with humoral factors known to influence their numbers:

Peripheral blood mononuclear cells were obtained and stained for FACS analysis with antibodies to CD34, CD45, CD133, and KDR and the remaining cells grown under endothelial cell conditions for assessment of colony-forming unit (CFU) numbers and adhesive properties. Levels of circulating vascular endothelial growth factor (VEGF), erythropoietin (EPO), and C-reactive protein (CRP) were determined and correlated with each of the EPC markers.

Pathophysiology of cECs

The endothelium can be viewed as a membrane-like layer lining the circulatory system, its primary function being the maintenance of vessel wall permeability and integrity. The EC layer is relatively quiescent, with an estimated cell turnover period of between 47 and 23,000 days, as shown by labeling studies. Proliferation seems to occur mainly at sites of vasculature branching and turbulent flow. cECs are thought to have ‘‘sloughed off’’ vessel walls, indicating severe endothelial damage. Thus, unsurprisingly, cECs have been shown to correlate with various endothelial dysfunction and inflammatory markers.

Although not fully understood, it would appear that cECs detachment from the endothelium involves multiple factors, such as mechanical injury, alteration of endothelial cellular adhesion molecules (such as integrin alphaVbeta3), defective binding to anchoring matrix proteins (such as fibronectin, laminin, or type IV collagen), and cellular apoptosis with decreased survival of cytoskeletal proteins. The net effect is a reduced interaction between the EC and basement membrane proteins, with subsequent cellular detachment (Goon et al. 2006).

 

Pathophysiology of cEPCs

In Science 1997, Asahara et al. was the first to isolate EPC in human peripheral blood, using anti-CD34 monoclonal antibodies. With the use of CD133, an antigen specifically identifying primitive stem cells, a novel means to precisely delineate mature (cECs) from immature (cEPCs) EC forms was possible (Asahara et al. 1997), although this antigen is only present in human EPCs and cannot be applied to mouse EPCs (Rafii et al. 2003). To detect cEPCs in peripheral blood, Flow Cytometry and culture have become the principal methods employed. Other markers used include vWf, VE-cadherin, vascular endothelial growth factor receptor-2 (VEGFR-KDR) and binding by lectins and acetylated low-density lipoproteins (Peichev et al. 2000, Rafii et al. 2003).

cEPCs are potentially crucial for neovascularization and may be recruited from the bone marrow after tissue ischemia, vascular insult, or tumor growth (Rafii et al. 2003). They possess the ability to migrate, colonize, proliferate, and, ultimately, differentiate into endothelial lineage cells. These cells have yet to acquire mature ECs characteristics while appearing to contribute to vascular homeostasis.

cEPCs have been isolated previously from human umbilical cord blood, adult bone marrow, human fetal liver cells, and cytokine-mobilized peripheral blood, and an increase in cEPCs follows in vivo administration of the angiogenic growth factor VEGF. When incubated with VEGF, fibroblast growth factor-2 (FGF-2), and insulin-like growth factor, CD133+ cells differentiated into mature-type adherent EC, expressing endothelial-specific cell markers (vWf and VE-VE cadherin) and abolishing CD133 expression (Goon, 2006). Generation of endothelial outgrowths that are positive for CD146, vWf (mature endothelial growth markers), and CD36 (a representative scavenger receptor marker as well as a microvascular marker) markers from circulating mononuclear cells (of donor genotype in bone marrow transplant patients), strongly suggests the viability and proliferative potential of cEPCs.

cEPCs recruitment and mobilization have been positively correlated with increased levels of angiogenic growth factors such as VEGF which induces the proliferation, differentiation, and chemotaxis of cEPCs, and is essential for hematopoiesis, angiogenesis, and, ultimately, survival.  cEPCs influence cells mainly by interactions with VEGFR-1 and VEGFR-2, both being receptors expressed on hematopoietic stem cells (HSC) and cEPCs. In another study, granulocyte colony-colony stimulating factor also increased the number of CD34 stimulating CD34+ cells, potentially stimulating neovascularization in areas of is- ischemic myocardium Other angiogenic growth factors stimulating cEPCs mobilization include angiopoietin-1, FGF, SDF-1, PlGF, and (in mice) macrophage colony-stimulating factor. After mobilization, cEPCs appear to “home in” and become incorporated into sites of vascular injury and ischemia, with evidence of improvement in the function and viability of tissue (e.g., after acute myocardial infarction) (Kocher et al. 2001).

Chemotactic agents responsible for this process include VEGF and SDF-1, but others may also be involved. In the clinical setting, moderate exercise of patients with stable coronary artery diseases leads to a significant increase in cEPCs (Laufs et al. 2004). Furthermore, cEPCs and HSC introduced into the circulation of acute and chronic cardiovascular disease patients through injection have shown vascular encouraging preliminary results, with evidence of improved cardiovascular function and tissue perfusion Tse et al. (2003); as of yet, there are no randomized control trial!

Recent reports suggest that cECs and cEPCs enumeration can be used to monitor antiangiogenesis drug therapy with some success. This exciting prospect needs to be fully corroborated in a clinical setting. In addition, cECs and cEPCs monitoring would need to be efficient, specific, robust, and reproducible. Therefore, it is vital to reach a general consensus regarding definitions and techniques for cECs and cEPCs quantification, in order to validate further reports that have implications for future clinical trials involving these markers (Goon, 2006).

In 2002, matrix metalloproteinase-9 (MMP-9) was identified as the molecular key to the release of EPCs from the bone-marrow compartment via cleavage of membrane kit ligand (Heissig et al., 2002). MMP-9 activity has also been shown to be upregulated by SDF-1alpha, VEGF, and hypoxia. Hypoxia is a potent stimulus for neovascularization, ischemia-induced growth, EPC trafficking and upregulation, vascular malformations and malignant endothelial cell tumors. This include activation of two upstream mediators of vasculogenesis, SDF-1 alpha and MMP-9, during the proliferative phase via EPC mediated vasculogenesis when these stem cells may rapidly proliferate in the ischemic tissue resulting in growth.

How a mobilized population of progenitor cells homes to ischemic tissue under repair was examined using bone-marrow transplantation studies. Following this procedure, reconstitution is regulated by chemokine ligand-receptor pair, stromal-cell derived factor 1 (SDF-1) and CXCR4 (Lapidot & Petit, 2002 reporting their discovery of 1999). EPCs express CXCR4, CXCR4/SDF-1 signal for EPC homing to peripheral sites of neovascularization. EPC SDF-1alpha expression was increased in proportion to reduced oxygen tension and this correlated with EPC localization in the most ischemic tissue sections (Kleinman, et al. 2005).

Table 1: Humoral factors known to influence eCPCs numbers

CD34 CD45 CD133 KDR CD34/KDRMost appropriate Definition of cEPCs CD34/CD133/KDR CD34/CD133 Adhesive properpies
VEGF level corr Positive correlation
EPO
CRP
CFU Colony forming unit numbersReflects cEPCs ability to proliferate No corr No corr Negative correlation Positive correlation
Adhesive properties No corr No corr No corr No corr
CD34
CD45
CD133
KDR
CD34/CD133/KDR Positive correlation
CD34/CD133 No corr

 SOURCE:

Table 1 is constructed from data in George et al. (2005),(2006) who concluded that current methods for quantitatively assessing numbers of circulating EPC are not correlated. VEGF serum levels are associated only with CD34/KDR and CD34/ CD133/KDR, whereas CFU numbers correlate with EPC functional properties. These findings may suggest that CD34/KDR is more appropriate for the definition of circulating EPC, whereas CFU numbers are more likely to reflect their ability to proliferate.

 

Trans-Endothelium Cell Migration

Lapidot and Petit in a recent review of the stem cell mobilization research field concluded that the following are the seminal processes at work in the facilitation of transendothelium cell migration. These processes could mediate stem cell release and remodeling of the bone marrow microenvironment, followed by stem cell migration via the circulation, homing back to the bone marrow and repopulation of damaged/restructured sites in an organ as part of the continuous replenishment of the blood with new immature and maturing cells while maintaining undifferentiated stem cells (Lapidot and Petit, 2002).

  •       Regulation of hematopoietic stem cell release, migration, and homing to the bone marrow, as well as the mechanism of different mobilization pathways, involve a complex interplay between adhesion molecules, chemokines, cytokines, proteolytic enzymes, stromal cells, and hematopoietic cells, the mechanism is not fully understood;
  •       The chemokine, stromal derived factor-1 (SDF-1)and its receptor CXCR4 play a major role in stem cell mobilization, including granulocyte colony-stimulating factor (G-CSF) and G-CSF with the chemotherapeutic agents cyclophosphamide Cy-induced mobilization, as well as in stem cell homing to the bone marrow and anchorage (i.e., activation of adhesion interactions in order to retain stem cells within the organ).
  •       They suggested that in addition to SDF-1 degradation and inactivation within the bone marrow by proteolytic enzymes such as neutrophil elastase, which is essential for optimal stem cell mobilization, interactions between this chemokine and its receptor are also needed for stem cell release and mobilization. For example, they suggested that IL-8, which is secreted in response to SDF-1 stimulation, and MMP-2 and MMP-9, which are mostly secreted by neutrophils but are also secreted by immature human CD34+ progenitor cells in response to stimulation with this chemokine, can also lead to migration away from the bone marrow across the endothelium into the circulation also in the absence of or against a gradient of SDF-1 under shear flow forces within the extravascular space of the bone marrow (Cinamon et al., 2001).
  •        They suggest that in order to maintain stem cells in the circulation low levels of surface CXCR4 are required and may be achieved by factors in the blood plasma such as proteolytic enzymes that can also cleave CXCR4 in addition to SDF-1 . Valenzuela-Fernandez (2002). Furthermore, increase in the levels of CXCR4 expression on the surface of stem cells in the circulation will mediate their homing and reengraftment of the bone marrow as part of homeostatic regulation of leukocyte trafficking as well as steady-state hematopoiesis and stem cell self-renewal, which go hand in hand with bone destruction and bone remodeling. However, this hypothesis is also an oversimplification of a much more complex and dynamic situation with physiological steady-state homeostatic as well as stress-induced mobilization situations in which the mechanisms and mode of regulation are still poorly understood.
  •        A significant number of studies in the past few years have revealed insights into regulation of hematopoietic stem cell release, migration, and homing as well as the mechanism of different mobilization pathways. However, the exact sequence of events involving many different molecules is still not clear. More importantly, in addition to results from clinical mobilization protocols using Cy and G-CSF, which demonstrate a role for SDF-1 and CXCR4 interactions in immature human CD34+ cell mobilization, two recent reports also demonstrate a role for these interactions in autologous and allogenic CD34+ cell homing and repopulation.
  •        Taken together, these results suggest that stem cell homing and release or mobilization are mirror images utilizing a similar mechanism and suggest manipulation of SDF-1/CXCR4 interactions in order to improve stem cell mobilization or to target migration of transplanted cells to specific organs. These results strongly support the idea that increasing the migration potential of immature human CD34+ cells prior to transplantation, either by short term stimulation with SCF and IL-6 and/or by cotransplantation with accessory cells. It could also increase homing and repopulation in transplanted patients, leading to improved treatment efficiencies and cure rates in clinical protocols.

 

Prospects and Limitations of Exogenous methods for cEPCs Augmentation

ElectEagle represents a conceptual formulation for several strategies to increase cEPCs number endogenously.

Additional posts on this Scientific Web Site on related topics are:

Lev-Ari, A., (2012S). Endothelial Dysfunction, Diminished Availability of cEPCs, Increasing CVD Risk for Macrovascular Disease – Therapeutic Potential of cEPCs

http://pharmaceuticalintelligence.com/2012/08/27/endothelial-dysfunction-diminished-availability-of-cepcs-increasing-cvd-risk-for-macrovascular-disease-therapeutic-potential-of-cepcs/

Lev-Ari, A., (2012T). Vascular Medicine and Biology: CLASSIFICATION OF FAST ACTING THERAPY FOR PATIENTS AT HIGH RISK FOR MACROVASCULAR EVENTS Macrovascular Disease – Therapeutic Potential of cEPCs

http://pharmaceuticalintelligence.com/2012/08/24/vascular-medicine-and-biology-classification-of-fast-acting-therapy-for-patients-at-high-risk-for-macrovascular-events-macrovascular-disease-therapeutic-potential-of-cepcs/

Below, this method is contrasted with exogenous methods involving the cell-based vascular therapy approaches currently applied for angiogenesis (mature cell-derived generation of new vessels), vasculogenesis (EPC-dependent generation of new vessels), neovascularization (ischemic tissue) and re-endothelialization (injured blood vessel.)  The majority of these methods are exogenous involving implantation or transplantation of various kinds: genetically engineered vein grafts, vascular bioprosthesis, retroviral transduction of genetic modifications to over-express a therapeutic gene(s).Despite the hurdles quoted below, the outlook for EPC-based therapy for cardiovascular disease is promising.Among the remaining outstanding issues in this fast growing research discipline, Dzau et al., chart a perspective for future research directions (Dzau et al. 2005)

“Despite the encouraging results regarding the therapeutic potential of EPCs, several issues currently stand in the way of their wide clinical application. Strategies need to be developed to enhance the number of EPCs to allow the harvesting of adequate number for therapeutic application. The limited ability to expand PB-MNC–derived EPCs in culture to yield sufficient number for clinical application indicates that alternative sources of cells (i.e., chord blood) or strategies to increase their number endogenously need to be explored. We believe that further characterization of the biology of EPCs, the nature of the mobilizing, migratory and homing signals, and the mechanisms of differentiation and incorporation into the target tissues need to be identified and further characterized. Strategies to improve retention and survival of the transplanted cells need to be developed as well. The issues of the timing of cell administration, the appropriate clinical condition, the optimal cell number, and, most importantly, the safety of cell transplantation must be defined. There is urgent need to standardize the protocols for isolation, cultivation, and therapeutic application for cell-based therapy. Finally, large-scale randomized, controlled, multi-centric trials will be essential to evaluate the long-term safety and efficacy of EPC therapy for treatment of tissue ischemia and vessel repair amid concerns of potential side effects such as neovascularization of occult neoplasias and the development of age- and diabetes-related vasculopathies. Despite these hurdles, the outlook for EPC-based therapies for tissue ischemia and blood vessel repair appears promising. Genetic engineering of EPC may provide an important strategy to enhance EPC mobilization, survival, engraftment, and function, thereby rendering these cells efficient therapeutic modalities for cardiovascular diseases.” (italics added).

In the Brief Review in Hypertension, Dzau et al., list several serious potential problems with therapeutic use of EPCs (Dzau et al. 2005)

“Although the preclinical and clinical studies reviewed here generally lend support to the therapeutic potential of autologous EPCs in the treatment of tissue ischemia and repair of injured blood vessels, the clinical application of EPCs is limited by several factors. First, the scarcity of cEPCs makes it difficulty to expand sufficient number of cells for therapeutic application without incurring the risk of cell senescence and change in phenotype (Asahara, et al., 1997, 1999). Furthermore, EPCs from patients with cardiovascular diseases display varying degrees of functional impairment (Vasa et al., 2001a, 2001b), (Hill et al., 2003), (Heeschen et al., 2004), (George et al., 2003), (Loomans et al., 2004), (Tepper et al., 2002). Aging and diabetes markedly reduce the availability and impair the function of EPCs (Hill et al., 2003), (Loomans et al., 2004), (Tepper et al., 2002), (Schatteman et al., 2000), (Scheubel et al., 2003), (Edelberg et al., 2002). Because older and diabetic patients are the most vulnerable populations for cardiovascular diseases, this severely restricts the ability to treat with autologous EPCs the patients who theoretically need them most.

The purity and developmental stage of the cells used for transplantation are important factors. Yoon et al reported recently that injection of total bone marrow cells into the heart of infarcted rats could potentially lead to severe intramyocardial calcifications (Yoon et al., 2004). In contrast, animals receiving the same number of clonally expanded bone marrow cells did not show myocardial calcification. Thus, this finding brings attention to the potential risks of transplanting unselected bone marrow cells and cautions against their premature use in the clinical setting.

Exogenous mobilization of bone marrow with hematopoietic growth factors and other endothelial cell growth factors may recruit progenitor cells to sites of occult neoplasia, leading to vascularization of dormant tumors. In addition, mobilization could potentially accelerate progression of atherosclerotic plaque by recruiting inflammatory and vascular smooth muscle cell progenitor cells into the plaque, contributing to neointima hyperplasia and transplant arteriopathy (Caplice et al., 2003), (Sata et al., 2002). Increased rate of in-stent restenosis led recently to the cancellation of the MAGIC clinical trial using G-CSF for endogenous mobilization of progenitor cells in patients with myocardial infarction.120 Finally, there has been one study that has shown evidence that EPC may themselves contribute to allograft vasculopathy by promoting neovascularization of the plaque(Hu et al., 2003). However, another study failed to show evidence that EPCs contribute significantly to transplant arteriosclerosis (Hillebrands et al., 2003).”

In accordance with this account is the latest review of EPC as therapeutic vectors in CV disorders covering experimental models and human trials (Ben-Shoshan and George, 2006).

The conceptual formulation for several strategies to increase cEPCs number endogenously presented in this investigation is complementary to methods currently applied or are still in clinical trials, as reviewed by Dzau et al. (2005). However, our approach, ElectEagle, involves endogenous augmentation of cEPCs by development of a concept-based protocol for therapeutic treatment using three components:

  •                Inhibition of ET1, ETB
  •                Induction of NO production and stimulation of eNOS
  •                Treatment Regimen with PPAR-gamma agonists (TZD) 

REFERENCES

Aicher A, Heeschen C, Mildner-Rihm C, Urbich C, Ihling C, Technau- Ihling K, Zeiher AM, Dimmeler S, (2003). Essential role of endothelial nitric oxide synthase for mobilization of stem cell and progenitor cells. Nat Med., 9:1370-1376.

Anderson T. (1999). Assessment of treatment of endothelial dysfunction. J Am Coll of Cardiology, 34: 631- 8.

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Endothelial Dysfunction, Diminished Availability of cEPCs,  Increasing  CVD Risk — Macrovascular Disease – Therapeutic Potential of cEPCs

Author and Investigator Initiated Study: Aviva Lev-Ari, PhD, RN

In normal conditions, the vascular endothelium produces and secretes substances that modulate vascular tone and protect the vessel wall from inflammatory cell infiltration, thrombus formation, and vascular smooth muscle cell proliferation (Rubanyi, 1993). Pathologic conditions such as hyperlipidemia, hyperglycemia, and hypertension impair the ability of the vascular endothelium to produce vasodilatory and anti-adhesion moieties and increase the production of vasoconstrictor, proadhesion, and pro-thrombotic molecules, leading to elevated vascular tone, enhanced cell adhesion, proliferation of media smooth muscle cells, and propensity toward thrombosis (Drexler & Hornig, 1999),(Endemann & Schiffrin, 2004). Endothelial cell loss and turnover are accelerated in the presence of hemodynamic and biochemical alterations and are a prominent feature of vascular injury resulting from percutaneous coronary intervention (Bennett & O’Sullivan, 2001).

The loss of endothelial function and integrity sets in motion the cascade of events that lead to atherosclerosis and restenosis after percutaneous revascularization (Ross, 1999),(Dzau et al., 2002). Processes of mobilization, growth, differentiation, recruitment, homing, replication and migration characterize cEPCs from the initial cell division of stem cells to cell apoptosis. What are the factors influencing cEPC mobilization, growth, differentiation, recruitment, mobilization, homing, replication and migration?

Physiological Factors

Chemokines

SCF-1, G-CSF, GM-CSF

Effect on cEPCs: recruitment, mobilization (Takahashi et al., 1999), (Kong et al., 2004a), (Kocher et al. 2001), (Shi et al., 1998), (Cho et al., 2003),(Orlic et al., 2001),(Bhattacharya et al., 2000), (Shi et al, 2002)

SDF-1

Effect on cEPCs: recruitment, mobilization, homing (Yamaguchi et al., 2003),(Powell et al., 2005),(Askari et al., 2003), (Hiasa et al., 2004),(George et al., 2003),(George et al., 2004),(Massa et al., 2005)

Cytokines / Growth Factors

FGF, VEGF, PIGF

Effect on cEPCs: mobilization, differentiation (Kalka et al., 2000a),(Ashara et al., 1997),(Kalka et al., 2000b)

                                  Angiopoietin, PDGF

Effect on cEPCs: differentiation

Hormones

Erythropoietin

Effect on cEPCs: mobilization, replication (Heeschen et al., 2003), (George, et. al., 2005).

Estrogen

Effect on cEPCs: mobilization (Strehlow et al., 2003), (Imanishi et al., 2005)

Signaling molecules

NO, Akt

Effect on cEPCs: mobilization, differentiation(Aicher et al., 2003).

 

Pharmacological Factors

3-HMC-CoA Inhibitors (statins)

Effect on cEPCs: mobilization, migration, homing (Werner et al., 2003),(Vasa et al., 2001a),(Walter et al., 2002),(Dimmeler et al., 2001),

(Llevadot et al., 2001),(Spyridopoulos et al., 2004)

             PPAR-gamma Agonists

Effect on cEPCs: mobilization, differentiation (Verma & Szmitko, 2006), (Andrew et al., 2004)

Physical Factors

 

            Exercise, hypoxia

Effect on cEPCs: mobilization (Laufs et al., 2003),(Kleinman et al., 2005),(Goon et al., 2006)

Pathological Factors

Coronary artery disease (CAD)

Effect on cEPCs: mobilization, homing (Kalka et al., 2000a),(Vasa et al., 2001b),(Heeschen et al., 2004)

Acute MI

Effect on cEPCs: mobilization, homing (Shintani et al., 2001),(Valgimigli et al., 2004),(Massa et al., 2005)

Peripheral limb ischemia

Effect on cEPCs: mobilization, homing (Takahashi et al., 1999),(Iwaguro et al., 2002),(Asahara et al., 1997),(Kalka et al., 2000b)

Vascular injury and inflammation

Effect on cEPCs: mobilization, homing (Ross, 1999),( Losordo et al., 2003), (Dimmeler & Zeiher, 2004),(Werner et al., 2003),(Verna et al, 2004).

EPC transplantation has been shown to induce new vessel formation in ischemic myocardium and hind limb (Kalka et al., 2000c),(Kawamoto et al, 2001),(Kocher, 2001) and to accelerate re-endothelialization of injured vessels and prosthetic vascular grafts in humans and in various animal models (Kocher, 2001),(Griese et al., 2003) demonstrating their therapeutic potential as a cell-based strategy for rescue and repair of ischemic tissues and injured blood vessels. Furthermore, EPCs are amenable to genetic manipulation, underscoring their usefulness as vectors for local delivery of therapeutic genes (Griese et al., 2003),(Kong et al., 2004b), (Iwaguro, 2002)

   Clinical Frontiers and Therapeutic Applications of cEPCs

  • Angiogenesis
  • Neovascularization of Artherosclerotic Plaque
  • Risk Factors impairing Collateral Development
  • Inhibitory Effects of Hypercholesterolemia
  • Bone Marrow Cells: Supporting cells in vascular growth processes
  • Inverse Relations: cEPCs and Risk of Macrovascular Events
  • New Stenting Technology:

 

  1.    Stents eluting Nitric Oxide (Verma and Marsden, 2005)
  2.    Stents coated with antiboby specific (anti-CD34) to the EPCs antigen cell     (Chadwick, 2006),(Aoki et al., 2005)
  3.    EPC-covered intravascular stents deployed for prevention of stent  thrombosis and restenosis as well as for rapid  formation of normal tissue architecture (Shirota et al., 2003).

 

  1. Table 1:            Alterations in number and function of cEPCs Disease Characterization and Suitability for ElectEagle an Endogenous Augmentation Method for cEPCs number (not for cEPCs function)

Disease Type

(Dzau et al., 2005)

Number

of

 cEPCs

Function

of

cEPCs

References

Disease Suitability for Endogenous Augmentation of cEPCs
Myocardial
     CAD

down

 down

(Kalka et al., 2000a),(Shintani et al., 2001),(Vasa et al., 2000b),(Hill et al., 2003),(Heeschen et al., 2004)

yes

     CHF

down

down

(Valgimigli et al.,2004),(Massa et al., 2005)

yes

     Unstable angina

down

unknown

(George et al., 2004)

yes

     MI

up

down

(Massa et al., 2005)

No

Vascular
     Atherosclerosis

down

down

(Vasa et al., 2001b),(Heeschen, 2004)(Lusis, 2000)

yes

     Acute Vascular injury and inflammation

up

unknown

(Fuujiyama et al.,2003)(Werner et al., 2003),(Walter et al., 2002),(Strehlow et al., 2003),(Shi et al., 1998),(Gill et al., 2001),

(Chu et al., 2003)

No

     PeripheralLimb ischemia

up

unknown

(Takahashi et al.,1999),(Iwaguro et al., 2002),(Asahara et al., 1997),(Asahara et al., 1999),(Kalka et al., 2000b)(Segal at al., 2006)

No

     Transplantarteriopathy

down

unknown

(Simper at al., 2003)

Yes

     In-stentrestenosis

down

unknown

(George et al., 2003)

yes

     Hypertension

unknown

unknown

No

     Hyperlipidemia

down

down

(Rauscher et al., 2003)

yes

Diabetes

down

down

(Loomans et al.,2004),(Tepper et al., 2002)

yes

Renal Failure
     Hemodialysis

down

down

(Choi et al., 2004)

yes

Source: original table created by Lev-Ari, A.

Based on Table 1, above, Lev-Ari, A. concluded that four Cardiovascualr diseases are NOT candidates for cEPCs therapeutic treatment

List of Disease unsuitable for ElectEagle an Endogenous Augmentation Method for  cEPCs includes:

  • Myocardial infarction
  • Acute Vascular injury and inflammation
  • Peripheral Limb ischemia
  • Hypertension

Table 2:           Therapeutic Angiogenesis Effects achieved by Cell-Based Therapy: Donor, Human; Recipient, Autologous;

Diagnosis, Myocardial Infarction

 

Therapeutic

Effect

Measured

Effect

Method of Delivery

Type and

Source of Cells

References

EjectionFruction

Up

(Stamm et al.,2003)

(Assmus et al., 2002),

(Britten et al., 2003),

(Schachinger et al., 2004),

(Wollert et al., 2004)

(Fernandez-Aviles

et al., 2004),

(Kang et al., 2004)

 

Infarct border

(Stamm et al., 2003)

CD133

(Stamm et al., 2003),

 

BM

(Stamm et al., 2003)

(Stamm et al., 2003)

Collateral flow (SPECT)

Up

(Stamm et al., 2003)

Infarct size

Down

(Strauer et al., 2002)

Intracoronary Balloon

Catheter

(Strauer et al., 2002)

BM

(Strauer et al., 2002)

(Strauer et al., 2002)

Wall motion

Up

(Strauer et al., 2002)

Contractility

Up

(Assmus et al., 2002),

(Britten et al., 2003),

(Schachinger et al., 2004),

(Wollert et al., 2004)

Intracoronary Balloon

Catheter

(Assmus et al., 2002),

(Britten et al., 2003),

(Schachinger et al., 2004),

(Wollert et al., 2004)

BM

PB

MNC

(Assmus et al., 2002),

(Britten et al., 2003),

(Schachinger et al., 2004),

(Wollert et al., 2004)

(Assmus et al., 2002),(Britten et al., 2003),(Schachinger et al., 2004),

(Wollert et al., 2004)

Myocardial perfusion

Up

(Assmus et al., 2002),

(Britten et al., 2003),

(Schachinger et al., 2004),

(Wollert et al., 2004)

Remodeling

Down

(Assmus et al., 2002),

(Britten et al., 2003),

(Schachinger et al., 2004),

(Wollert et al., 2004)

LV wall thickness

Up

(Fernandez-Aviles et al., 2004)

Intracoronary w/PCA

(Fernandez-Aviles et al., 2004)

CD34+

CD117+

AC133+

(Fernandez-Aviles et al., 2004)

End-systolic (ESV) volume

Down

(Fernandez-Aviles et al., 2004)

Exercise time

Up

(Kang et al., 2004)

Intracoronary

G-CSF

CD34+

(Kang et al., 2004)

 

Table 3:          

Therapeutic Angiogenesis Effects achieved by Cell-Based Therapy: Donor, Human; Recipient, Autologous;

Diagnosis, Myocardial Ischemia – Unstable Ischemia

 

Therapeutic

Effect

Measured

Effect

Method of Delivery

Type and

Source of Cells

References

Ejection Fruction

Up

(Perin et al., 2003),

(Tse et al., 2003)

Transendocardial with NOGA mapping

MNCs

(Perin et al., 2003),

(Tse et al., 2003)

BM

(Perin et al., 2003),

(Tse et al., 2003)

(Perin et al., 2003),

(Tse et al., 2003)

Anginal episodes

Down

(Perin et al., 2003),

(Tse et al., 2003)

Wall thickening

Up

(Perin et al., 2003),

(Tse et al., 2003)

Wall motion

Up

(Perin et al., 2003),

(Tse et al., 2003)

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Reporter: Aviva Lev-Ari, PhD, RN

Updated 3/10/2013

Since August 25, 2012, when the ESC: New Definition of MI Unveiled was reviewed by Robert Jasmer, MD; Associate Clinical Professor of Medicine, University of California, San Francisco as was reported  By Chris Kaiser, Cardiology Editor, MedPage Today,  a new discussion emerged by ACC asking if FFR CT is Ready for prime time or not?

By Lisa Fratt
Mar 09, 2013

SAN FRANCISCO—Is there a better way to measure fractional flow reserve (FFR), Bon-Kwon Koo, MD, of Seoul National University queried a crowded room March 9 during an educational session at the American College of Cardiology (ACC) scientific session.

The current model is good for patients, safe and effective, Koo said. However, it requires an invasive procedure and is expensive. FFR CT may provide a method to measure FFR without an invasive procedure.

FFRCT extracts geometry from a CT scan to determine boundary conditions and fluid properties. In addition, velocity and pressure can be calculated. The hitch is that a supercomputer is required to solve the blood flow equation, said Koo. The results provide anatomical and functional data, thus giving a possible answer to the question at hand.

FFRCT may change daily practice in several ways. Most importantly, it may be a novel, fast, risk-free, noninvasive cost-saving way to measure FFR and identify patients who may not need to be sent to the cath lab for stenting or PCI. It can provide information to help surgeons plan strategies before invasive procedures, bypass procedures or interventional procedures. Noninvasive CT-derived FFR also can predict the functional significance of coronary lesions.

Despite its promise, however, FFR CT is not ready for prime time, Koo said. FFR CT depends on the diagnostic accuracy of coronary CT angiography stenosis, which is less than true stenosis. With current technologies, true stenosis provides the required diagnostic accuracy.

FFRCT is promising, but further development of the technology is required, Koo concluded.

http://www.cardiovascularbusiness.com/topics/imaging/acc-ffrct—ready-prime-time-or-not

ESC: New Definition of MI Unveiled

By Chris Kaiser, Cardiology Editor, MedPage Today

Published: August 25, 2012

Reviewed by Robert Jasmer, MD; Associate Clinical Professor of Medicine, University of California, San Francisco

MUNICH — An international, multispecialty task force has published a new definition of myocardial infarction that was prompted by the new generation of highly sensitive cardiac troponin (cTn) assays.

The highly sensitive assays are capable of detecting cTn in conditions other than MI, such as pulmonary embolism, cardiomyopathy, and left bundle branch block, and so result in false positives, according to the task force writing group.

The expert consensus document dips into a controversial area by setting levels of cTn for MI associated with percutaneous coronary intervention (PCI) and coronary artery bypass grafting (CABG).

“This is one of the most controversial areas in the definition of myocardial infarction,” Anthony DeMaria, MD, from the University of California in San Diego and editor-in-chief of the Journal of the American College of Cardiology, told MedPage Today.

“There are a large number of people undergoing PCI in the setting of an acute MI. It’s almost impossible to know whether a subsequent increase in troponin was part and parcel of the acute MI or related to the procedure itself,” DeMaria said.

The consensus document, titled “Third Universal Definition of Myocardial Infarction,” set the cTn levels for MI associated with PCI as elevation of troponin greater than 5 times the 99th percentile upper reference limit (URL) in patients with normal baseline levels or a rise in troponin values greater than 20% if the baseline values are elevated and are stable or falling.

“Some people speculate that troponin may be too sensitive in this situation and what is needed is evidence that an elevation of some degree of troponin following a procedure actually results in some alteration of the natural history of the patient,” DeMaria said. “In other words, the definition of acute MI after a procedure really is of significance if it increases the risk of subsequent events such as death.”

In CABG, the task force set the troponin values as greater than 10 x 99th percentile URL during the first 48 hours when baseline values are normal.

DeMaria said there are several ongoing studies examining the correlation of elevated cTn with subsequent events. As this is the third definition of MI since 2000, there most likely will be more refinements as new data emerge, he said.

The document is being copublished online in several journals including the Journal of the American College of CardiologyCirculation, the European Heart Journal, and Global Heart.

The task force was in touch with the FDA during the development of this new definition, which means it could be used as the basis for clinical trial protocols designed according to FDA regulations.

“A universal definition for MI is of great benefit for clinical studies, since it will allow a standardized approach for interpretation and comparison across different trials,” the task force writing group explained.

When different definitions have been used in trials, it hampers “comparison and generalization between these trials,” they said.

Also of significance in this document is the inclusion of imaging as a means to identify or confirm an MI. The document spells out the strengths of echocardiography, nuclear imaging, MRI, and CT in the setting of acute MI.

“Imaging is playing an increasingly important role,” DeMaria said. “In the absence of focal symptoms or with an inconclusive ECG, it’s important to recognize the concomitant potential of ancillary measures, primarily imaging, to help with the diagnosis of a myocardial infarction.”

Thygesen reported relationships with Edwards Lifesciences, Servier, St. Jude Medical, Roche Pharma, and Roche Diagnostics. Her co-authors and reviewers reported relationships with Bayer Healthcare, Daiichi Sankyo, Johnson & Johnson, sanofi aventis, Servier, Novartis, Boehringer-Ingelheim, Genzyme, Eli Lilly, OrthoClinical Diagnostics, Abbott Laboratories, Alere, Brahms, Siemens Healthcare, Roche Pharma, Radiometer, BioRad, Diagenics, Response Medical, Takeda Pharmaceuticals, Regado Biosciences, Bristol-Myers Squibb, Merck Sharp and Dohme, GlaxoSmithKline, Merck, Portola Pharmaceuticals, AstraZeneca, Regado Biosciences, Scios, Ortho-Biotech, Pfizer, Kai Pharmaceuticals, Iroko Cardio, Philips, GE Healthcare, Boston Scientific, Lantheus, Medtronic, St. Jude Medical, Biotronik, Impulse Dynamics, Edwards Lifesciences, Health System Networks, Health Station Networks, Insight Telehealth Systems, Elsevier Sciences, Gilead, Evolva, Medicines Company, F. Hoffman La Roche, Torrent, Vifor International, Corthera, Nanosphere, Bayer Schering Pharma, Cardiorentis, Molecular Insight Pharmaceuticals, Berlin Chemie, Menarini, Cordis, Beckman Coulter, Amgen, Critical Diagnostics, Tethys Bioscience, Roche Diagnostics, bioMérieux, Genentech, Ikaria, Singulex, BG Medicine, Shionogi, Amylin, DiaDexus, Orion, WebMD, theheart.org, Pozen, Maquet, BHFZ, Covidien, Rapidscan, Actelion, Athera, Symetis, Schering-Plough, OrbusNeich, Terumo, Cardio3 Biosciences, Micell, Ablynx, Therabel, Kowa, Zentiva, Chugai Pharma, Automedics Medical Systems, Essentialis, Biosensors, Vascular Solutions, Zoll Medical, JaBA Recordati, Actavis, PharmaSwiss, Eisai, Medscape, Accumetrics, Bial Portela, AGA, Novo-Nordisk, Janssen-Cilag, Valtech, Otsuka Pharmaceuticals, Meda Pharma, CEPHALON, Intracellular Therapies USA, Santhera, TROPHOS, Pierre-Fabre, and Lundbeck.

DeMaria reported relationships with Gilead, ResMed Foundation, Lantheus, Cardiovascular Biotherapeutics, Angioblast Systems, General Electric Medical Systems, and Cardionet.

Primary source: European Heart Journal

Source reference:
Thygesen K, et al “Third universal definition of myocardial infarction” Eur Heart J 2012; DOI: 10.1093/eurheartj/ehs184.

ESC: FFR CT Has Potential for Tagging Ischemia

By Chris Kaiser, Cardiology Editor, MedPage Today

Published: August 26, 2012

Reviewed by Robert Jasmer, MD; Associate Clinical Professor of Medicine, University of California, San Francisco

MUNICH — Using CT imaging to assess the hemodynamic significance of coronary lesions is “promising” but needs more research before it displaces conventional invasive fractional flow reserve (FFR), researchers said.

Using FFR as the reference standard, FFRCTplus CT angiography (CTA) had good sensitivity (90%) and negative predictive value (84%) on a per patient basis for detecting ischemia, which indicates a low rate of false-negative studies, according to James K. Min, MD, of Cedars-Sinai Heart Institute in Los Angeles, and colleagues.

Although FFRCT plus CTA were superior to CTA alone, the specificity (54%) and negative predictive value (67%) of the combination remained low compared with conventional FFR, indicating that a considerable number of false-positive studies would endure, Min reported here during a Hot-Line session at the European Society of Cardiology meeting.

The results of this proof of concept study show that FFRCT can “impart considerable discriminatory power” to detect and exclude ischemia in patients with suspected CAD, Min said.

However, future studies should be conducted to determine the cost-effectiveness of FFRCT in guiding decisions to stent, particularly given the potentially high false-positive rate, he added.

“Non-invasive FFR is a dream for all interventional cardiologists,” said study discussant Jean-Pierre Bassand, MD, of the University Hospital Jean-Minjoz in Besançon, France. Although Bassand praised the DeFACTO study, he expressed concern about the discrepancy between the accuracy of FFR versus FFRCT.

For example, compared with FFR, the sensitivity and specificity of FFRCT in cases of greater than 90% or less than 30% stenosis were 83% and 76%, respectively. The per-vessel correlation of FFRCT to FFR was 0.63.

“What matters is the correlation with FFR,” he concluded.

A single non-invasive imaging test that can identify obstructive coronary artery disease (CAD) and determine the physiological significance of those lesions would be ideal. At present, nuclear stress imaging fulfills the first part, but it cannot label stenoses as hemodynamically significant or not. Also, nuclear stress testing suffers from high rates of both false-negative and false-positive studies, Min said.

The results of this study are in line with stress imaging: per patient diagnostic accuracy of 73% (95% CI 67% to 78%). Min said that studies are being designed to compare FFRCT plus CTA with stress imaging.

“For patients considered for invasive therapy, this type of test could help exclude those who don’t need to be stented,” Spencer King III, MD, of St. Joseph’s Hospital in Atlanta told MedPage Today.

“The excitement about this CT approach is that it moves things closer to being able to assess physiology and anatomy in a single non-invasive test,” added King, who is also a past president of the American College of Cardiology.

However, the process of calculating the FFR values from CT data currently takes about 6 hours, Min told MedPage Today. The CT data are sent offsite to HeartFlow, the company that makes the software. Whether such processing would be done onsite in the future is not yet determined, Min said. He also expects the processing time to drop to about 2 hours by the year’s end.

HeartFlow has already received EU mark to use the software in Europe and is in the process of applying for FDA approval, Min said.

Conventional FFR uses a pressure wire inserted through the groin to the coronary arteries to determine the hemodynamic significance of lesions. The same data can be gleaned during a typical CTA exam with software that calculates computational fluid dynamics,without additional radiation exposure. The median radiation exposure among the study centers was 6.4 mSv (range 4.4 to 15 mSv).

The original FAME study found the use of FFR to guide stenting was better than relying on angiography alone in patients with multivessel disease. A second study, FAME II, was stopped early because of the overwhelming benefit seen in patients with stable CAD when FFR guided stenting versus patients randomized to optimal medical therapy.

Because FFRCT is a novel technique, it has not been adequately evaluated in its ability to identify patients with ischemia, Min said.

The researchers therefore designed the DeFACTO (Determination of Fractional Flow Reserve by Anatomic Computed Tomographic Angiography) study, which sought to evaluate the accuracy of FFRCT while using invasive FFR as the reference standard.

The study was also simultaneously published online in the Journal of the American Medical Association.

The 252 patients with suspected or known CAD were recruited from 17 centers in five countries between October 2010 and October 2011. They were scheduled to undergo diagnostic catheter angiography.

The mean age of patients was 63, 70% were men, and a majority were white. Nearly half of the patients had obstructive CAD (>50% stenosis).

Among 615 study vessels, 271 had less than 30% stenosis and 101 had at least 90% stenosis. Invasive coronary angiography and FFR identified 46.5% of 408 vessels with obstructive CAD, while CT and FFRCT identified 52.3% of 406 vessels.

A total of 172 patients had an FFR value <0.80, which indicates an ischemic lesion.

The diagnostic accuracy of FFRCT plus CT was 73% (95% CI 67% to 78%), but this did not meet the prespecified primary endpoint of greater than 70% of the lower bound of the 95% confidence interval, Min said.

However, Min emphasized that FFRCT was superior to CTA alone in all categories.

The researchers concluded that the results show the potential of FFRCT as a “promising” non-invasive tool to identify ischemia.

King added that despite not meeting the prespecified primary endpoint, “it’s an encouraging early study.”

This study was funded by HeartFlow

Min reported relationships with GE Healthcare and Philips Medical. Some of his co-authors reported relationships with GE Healthcare, Siemens Medical Systems, Lantheus Medical Imaging, Boston Scientific, Merck, Abbott Vascular, Medtronic, Cordis, Eli Lilly, Daiichi Sankyo, Bristol-Myers Squibb, and sanofi-aventis.

King reporeted relationships with Merck & Company, Wyeth Pharmaceuticals, Celonova Biosciences, and Northpoint Domain.

 

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