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Archive for the ‘Population Health Management, Genetics & Pharmaceutical’ Category

Reporter:  Aviva Lev-Ari, PhD, RN

Call for Open-Access Publishing in Genomics

January 14, 2013

SAN DIEGO (GenomeWeb News) – Open-access datasets, software, and bioinformatics strategies have become more or less de rigueur in genomics research.

But the field may also be poised to change the way other sorts of information from scientific studies is conveyed to other researchers and to the broader public, according to open-access proponent Michael Eisen, a computational and evolutionary biology researcher at the University of California, Berkeley.

Eisen, a Public Library of Science co-founder, spoke during the morning plenary session here at the International Plant and Animal Genome Conference.

In his presentation, he argued that the inability to freely and unreservedly access the full text of all genome studies performed to date may have led to missed opportunities for the field.

Using the bacteriophage phiX174 genome sequence as an example, he proposed that the general thinking in the genomics field has developed in ways that promote open-access to sequence data and related software. But, he said, the same type of access is not necessarily available for those interested in delving into the details and rationale behind genomics studies, since the corresponding papers may not be accessible in an open-access format.

The UK Medical Research Council Laboratory of Molecular Biology‘s Frederick Sanger and colleagues described the phiX174 sequence in 1977, in a publication that’s generally considered to be the first genome paper. The sequence data presented in that study is now freely available, Eisen explained, in part owing to the advent of sequence databases such as the European Molecular Biology Laboratory Nucleotide Sequence database or the National Center for Biotechnology Information’s sequence database, GenBank.

During the past decade or more, funding agency requirements and pressure from within the genomics community have contributed to the widespread adoption of these and other public genomics resources and repositories.

As these databases have grown and become accepted within the genomics community, Eisen argued that they have spurred the development of computational methods for analyzing genome sequences and datasets that may not have existed otherwise. “Imagine where we would be had we not made the fortunate decision to liberate genome sequences,” he said.

But analogous strategies for combing through text from genomics studies in their entirety have not developed in the same manner, according to Eisen, who noted that the text of the phiX174 genome paper remains behind a pay wall.

“We’ve allowed [journal access] and [data access] to follow very different fates,” said Eisen, who says there are ways to use the information housed within the scientific literature more easily and productively.

He urged attendees to consider publishing their own work in open-access publications. Beyond that, though, Eisen also noted that the community is well positioned to influence the ways in which research information is disseminated, since genomics data increasingly serves as a resource for other spheres of research.

 

 

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

Germline stem cells that produce oocytes in vitro and fertilization-competent eggs in vivo have been identified in and isolated from adult mouse ovaries. A fluorescence-activated cell sorting-based protocol has been standardized that can be used with adult mouse ovaries and human ovarian cortical tissue to purify rare mitotically active cells that have a gene expression profile that is consistent with primitive germ cells. Once established in vitro, these cells can be expanded for months and can spontaneously generate 35- to 50-μm oocytes, as determined by morphology, gene expression and haploid (1n) status. Injection of the human germline cells, engineered to stably express GFP, into human ovarian cortical biopsies leads to formation of follicles containing GFP-positive oocytes 1–2 weeks after xenotransplantation into immunodeficient female mice. Therefore, based on the multiple experimental lines of evidence reported it is reasonable to conclude that the rare cells with cell-surface expression of DDX4 that are present in the ovaries of reproductive-age women represent adult human OSCs. In addition to opening a new research field in human reproductive biology that was inconceivable less than 10 years ago, clear evidence for the existence of these cells in women may offer new opportunities to expand on and enhance current fertility-preservation strategies. For example, with assisted reproductive technologies involving cryopreservation of ovarian cortical tissue already in development for females with cancer, isolation and expansion of OSCs from this tissue before or after cryopreservation might be useful for new fertility applications. In fact, it has been found that these cells can be consistently obtained from cryopreserved and thawed human ovarian tissue samples, and that these cells per se can be cryopreserved and thawed months later with minimal loss for successful establishment in vitro. In addition, the availability of a detailed protocol for the purification of these newly discovered cells from human ovary tissue provides a much more physiologically relevant in-vitro model system from which to study human female germ cell development compared to the ESC-derived or induced pluripotent stem cell-derived germline cells that are currently used as models for human female gametogenesis.

Source References:

http://blogs.nature.com/spoonful/2012/02/video-stem-cell-discovery-puts-women%E2%80%99s-reproduction-on-fertile-grounds.html

http://www.nature.com/nm/journal/v18/n3/full/nm.2669.html

http://www.ncbi.nlm.nih.gov/pubmed/23024060

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Consumer Market for Personal DNA Sequencing: Part 4

Reporter: Aviva Lev-Ari, PhD RN

FDA Warning for the Leader of Consumer Market for Personal DNA Sequencing Part 4

Word Cloud by Daniel Menzin

This Part 4 of the series on Present and Future Frontier of Research in Genomics has been 

UPDATED on 12/6/2013

23andMe Suspends Health Interpretations

December 06, 2013

Direct-to-consumer genetic testing company 23andMe hasstopped offering its health-related test to new customers, bringing it in line with a request from the US Food and Drug Administration.

In letter sent on Nov. 22, FDA said that 23andMe had not adequately responded to its concerns regarding the validity of their Personal Genome Service. The letter instructed 23andMe to “immediately discontinue marketing” the service until it receives authorization from the agency.

According to a post at the company’s blog from CEO Anne Wojcicki, 23andMe customers who purchased their kits on or after Nov. 22 “will not have access to health-related results.” They will, though, have access to ancestry information and their raw genetic data. Wojcicki notes that the customers may have access to the health interpretations in the future depending on FDA marketing authorization. Those customers are also being offered a refund.

Customers who purchased their kits before Nov. 22 will have access to all reports.

“We remain firmly committed to fulfilling our long-term mission to help people everywhere have access to their own genetic data and have the ability to use that information to improve their lives,” a notice at the 23andMe site says.

In a letter appearing in the Wall Street Journal earlier this week, FDA Commissioner Margaret Hamburg wrote that the agency “supports the development of innovative tests.” As an example, she pointed to its recent clearance of sequencing-based testsfrom Illumina.

She added that the agency also understands that some consumers do want to know more about their genomes and their genetic risk of disease, and that a DTC model would let consumers take an active role in their health.

“The agency’s desire to review these particular tests is solely to ensure that they are safe, do what they claim to do and that the results are communicated in a way that a consumer can understand,” Hamburg said.

In a statement, 23andMe’s Wojcicki says that the company remains committed to its ethos of allowing people access to their genetic information. “Our goal is to work cooperatively with the FDA to provide that opportunity in a way that clearly demonstrates the benefit to people and the validity of the science that underlies the test,” Wojcicki adds.

SOURCE

UPDATED on 11/27/2013

FDA Tells Google-Backed 23andMe to Halt DNA Test Service

VIEW VIDEO

http://www.bloomberg.com/news/2013-11-25/fda-tells-google-backed-23andme-to-halt-dna-test-service.html

FDA Letter to 23andME

Department of Health and Human Services logoDepartment of Health and Human Services

Public Health Service
Food and Drug Administration
10903 New Hampshire Avenue
Silver Spring, MD 20993

Nov 22, 2013

Ann Wojcicki
CEO
23andMe, Inc.
1390 Shoreline Way
Mountain View, CA 94043
Document Number: GEN1300666
Re: Personal Genome Service (PGS)
WARNING LETTER
Dear Ms. Wojcicki,
The Food and Drug Administration (FDA) is sending you this letter because you are marketing the 23andMe Saliva Collection Kit and Personal Genome Service (PGS) without marketing clearance or approval in violation of the Federal Food, Drug and Cosmetic Act (the FD&C Act).
This product is a device within the meaning of section 201(h) of the FD&C Act, 21 U.S.C. 321(h), because it is intended for use in the diagnosis of disease or other conditions or in the cure, mitigation, treatment, or prevention of disease, or is intended to affect the structure or function of the body. For example, your company’s website at http://www.23andme.com/health (most recently viewed on November 6, 2013) markets the PGS for providing “health reports on 254 diseases and conditions,” including categories such as “carrier status,” “health risks,” and “drug response,” and specifically as a “first step in prevention” that enables users to “take steps toward mitigating serious diseases” such as diabetes, coronary heart disease, and breast cancer. Most of the intended uses for PGS listed on your website, a list that has grown over time, are medical device uses under section 201(h) of the FD&C Act. Most of these uses have not been classified and thus require premarket approval or de novo classification, as FDA has explained to you on numerous occasions.
Some of the uses for which PGS is intended are particularly concerning, such as assessments for BRCA-related genetic risk and drug responses (e.g., warfarin sensitivity, clopidogrel response, and 5-fluorouracil toxicity) because of the potential health consequences that could result from false positive or false negative assessments for high-risk indications such as these. For instance, if the BRCA-related risk assessment for breast or ovarian cancer reports a false positive, it could lead a patient to undergo prophylactic surgery, chemoprevention, intensive screening, or other morbidity-inducing actions, while a false negative could result in a failure to recognize an actual risk that may exist. Assessments for drug responses carry the risks that patients relying on such tests may begin to self-manage their treatments through dose changes or even abandon certain therapies depending on the outcome of the assessment. For example, false genotype results for your warfarin drug response test could have significant unreasonable risk of illness, injury, or death to the patient due to thrombosis or bleeding events that occur from treatment with a drug at a dose that does not provide the appropriately calibrated anticoagulant effect. These risks are typically mitigated by International Normalized Ratio (INR) management under a physician’s care. The risk of serious injury or death is known to be high when patients are either non-compliant or not properly dosed; combined with the risk that a direct-to-consumer test result may be used by a patient to self-manage, serious concerns are raised if test results are not adequately understood by patients or if incorrect test results are reported.
Your company submitted 510(k)s for PGS on July 2, 2012 and September 4, 2012, for several of these indications for use. However, to date, your company has failed to address the issues described during previous interactions with the Agency or provide the additional information identified in our September 13, 2012 letter for(b)(4) and in our November 20, 2012 letter for (b)(4), as required under 21 CFR 807.87(1). Consequently, the 510(k)s are considered withdrawn, see 21 C.F.R. 807.87(1), as we explained in our letters to you on March 12, 2013 and May 21, 2013.  To date, 23andMe has failed to provide adequate information to support a determination that the PGS is substantially equivalent to a legally marketed predicate for any of the uses for which you are marketing it; no other submission for the PGS device that you are marketing has been provided under section 510(k) of the Act, 21 U.S.C. § 360(k).
The Office of In Vitro Diagnostics and Radiological Health (OIR) has a long history of working with companies to help them come into compliance with the FD&C Act. Since July of 2009, we have been diligently working to help you comply with regulatory requirements regarding safety and effectiveness and obtain marketing authorization for your PGS device. FDA has spent significant time evaluating the intended uses of the PGS to determine whether certain uses might be appropriately classified into class II, thus requiring only 510(k) clearance or de novo classification and not PMA approval, and we have proposed modifications to the device’s labeling that could mitigate risks and render certain intended uses appropriate for de novo classification. Further, we provided ample detailed feedback to 23andMe regarding the types of data it needs to submit for the intended uses of the PGS.  As part of our interactions with you, including more than 14 face-to-face and teleconference meetings, hundreds of email exchanges, and dozens of written communications, we provided you with specific feedback on study protocols and clinical and analytical validation requirements, discussed potential classifications and regulatory pathways (including reasonable submission timelines), provided statistical advice, and discussed potential risk mitigation strategies. As discussed above, FDA is concerned about the public health consequences of inaccurate results from the PGS device; the main purpose of compliance with FDA’s regulatory requirements is to ensure that the tests work.
However, even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses, which have expanded from the uses that the firm identified in its submissions. In your letter dated January 9, 2013, you stated that the firm is “completing the additional analytical and clinical validations for the tests that have been submitted” and is “planning extensive labeling studies that will take several months to complete.” Thus, months after you submitted your 510(k)s and more than 5 years after you began marketing, you still had not completed some of the studies and had not even started other studies necessary to support a marketing submission for the PGS. It is now eleven months later, and you have yet to provide FDA with any new information about these tests.  You have not worked with us toward de novo classification, did not provide the additional information we requested necessary to complete review of your 510(k)s, and FDA has not received any communication from 23andMe since May. Instead, we have become aware that you have initiated new marketing campaigns, including television commercials that, together with an increasing list of indications, show that you plan to expand the PGS’s uses and consumer base without obtaining marketing authorization from FDA.
Therefore, 23andMe must immediately discontinue marketing the PGS until such time as it receives FDA marketing authorization for the device. The PGS is in class III under section 513(f) of the FD&C Act, 21 U.S.C. 360c(f). Because there is no approved application for premarket approval in effect pursuant to section 515(a) of the FD&C Act, 21 U.S.C. 360e(a), or an approved application for an investigational device exemption (IDE) under section 520(g) of the FD&C Act, 21 U.S.C. 360j(g), the PGS is adulterated under section 501(f)(1)(B) of the FD&C Act, 21 U.S.C. 351(f)(1)(B).  Additionally, the PGS is misbranded under section 502(o) of the Act, 21 U.S.C. § 352(o), because notice or other information respecting the device was not provided to FDA as required by section 510(k) of the Act, 21 U.S.C. § 360(k).
Please notify this office in writing within fifteen (15) working days from the date you receive this letter of the specific actions you have taken to address all issues noted above. Include documentation of the corrective actions you have taken. If your actions will occur over time, please include a timetable for implementation of those actions. If corrective actions cannot be completed within 15 working days, state the reason for the delay and the time within which the actions will be completed. Failure to take adequate corrective action may result in regulatory action being initiated by the Food and Drug Administration without further notice. These actions include, but are not limited to, seizure, injunction, and civil money penalties.
We have assigned a unique document number that is cited above. The requested information should reference this document number and should be submitted to:
James L. Woods, WO66-5688
Deputy Director
Patient Safety and Product Quality
Office of In vitro Diagnostics and Radiological Health
10903 New Hampshire Avenue
Silver Spring, MD 20993
If you have questions relating to this matter, please feel free to call Courtney Lias, Ph.D. at 301-796-5458, or log onto our web site at www.fda.gov for general information relating to FDA device requirements.
Sincerely yours,
/S/
Alberto Gutierrez
Director
Office of In vitro Diagnostics
and Radiological Health
 Center for Devices and Radiological Health

SOURCE

http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm

Cancer Diagnostics by Genomic Sequencing: ‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

Symposia

http://aaas.confex.com/aaas/2013/webprogram/start.html

Personal Genetics: An Intersection Between Science, Society, and Policy

Saturday, February 16, 2013: 8:30 AM-11:30 AM

Room 203 (Hynes Convention Center)

On 26 June 2000, scientists announced the completion of a rough draft of the human genome, the result of the $3 billion publicly funded Human Genome Project. In the decade since, the cost of genome sequencing has plummeted, coinciding with the development of deep sequencing technologies and allowing, for the first time, personalized genetic medicine. The advent of personal genetics has profound implications for society that are only beginning to be discussed, even as the technologies are rapidly maturing and entering the market. This symposium will focus on how the genomic revolution may affect our society in coming years and how best to reach out to the general public on these important issues. How has the promise of genomics, as stated early in the last decade, matched the reality we observe today? What are the new promises — and pitfalls — of genomics and personal genetics as of 2013? What are the ethical implications of easy and inexpensive human genome sequencing, particularly with regard to ownership and control of genomic datasets, and what stakeholder interests must be addressed? How can the scientific community engage with the public at large to improve understanding of the science behind these powerful new technologies? The symposium will comprise three 15-minute talks from representatives of relevant sectors (academia/education, journalism, and industry), followed by a 45-minute panel discussion with the speakers.

Organizer:

Peter Yang, Harvard University

Co-organizers:

Brenna Krieger, Harvard University

and Kevin Bonham, Harvard University

Discussant:

James Thornton, Harvard University

Speakers:

 

Ting Wu, Harvard University

Personal Genetics and Education

Mary Carmichael, Boston Globe

The Media and the Personal Genetics Revolution

Brian Naughton, 23andMe Inc.

Commercialization of Personal Genomics: Promise and Potential Pitfalls

Mira Irons, Children’s Hospital Boston

Personal Genomic Medicine: How Physicians Can Adapt to a Genomic World

Sheila Jasanoff, Harvard University

Citizenship and the Personal Genomics

Jonathan Gitlin, National Human Genome Research Institute

Personal Genomics and Science Policy

THIS IS A SERIES OF FOUR POINTS OF VIEW IN SUPPORT OF the Paradigm Shift in Human Genomics

How to Tailor Cancer Therapy to the particular Genetics of a patient’s Cancer

‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities PRESENTED in the following FOUR PARTS. Recommended to be read in its entirety for completeness and arrival to the End Point of Present and Future Frontier of Research in Genomics

Part 1:

Research Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine

http://pharmaceuticalintelligence.com/2013/01/13/paradigm-shift-in-human-genomics-predictive-biomarkers-and-personalized-medicine-part-1/

Part 2:

LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment

http://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-drug-selection-in-cancer-personalized-treatment-part-2/

Part 3:

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research

http://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical-research-part-3/

Part 4:

The Consumer Market for Personal DNA Sequencing

 

Part 4:

The Consumer Market for Personal DNA Sequencing

How does 23andMe genotype my DNA?

Technology and Standards

23andMe is a DNA analysis service providing information and tools for individuals to learn about and explore their DNA. We use the Illumina OmniExpress Plus Genotyping BeadChip (shown here). In addition to the variants already included on the chip by Illumina, we’ve included our own, customized set of variants relating to conditions and traits that are interesting. Technical information on the performance of the chip can be found on Illumina’s website.

All of the laboratory testing for 23andMe is done in a CLIA-certified laboratory.

Once our lab receives your sample, DNA is extracted from cheek cells preserved in your saliva. The lab then copies the DNA many times — a process called “amplification” — growing the tiny amount extracted from your saliva until there is enough to be genotyped.

In order to be genotyped, the amplified DNA is “cut” into smaller pieces, which are then applied to our DNA chip, a small glass slide with millions of microscopic “beads” on its surface (read more about this technology). Each bead is attached to a “probe”, a bit of DNA that matches one of the approximately one million genetic variants that we test. The cut pieces of your DNA stick to the matching DNA probes. A fluorescent signal on each probe provides information that can tell us which version of that genetic variant your DNA corresponds to.

Although the human genome is estimated to contain about 10-30 million genetic variants, many of them are correlated due to their proximity to each other. Thus, one genetic variant is often representative of many nearby variants, and the approximately one million variants on our genotyping chip provide very good coverage of common variation across the entire genome.

Our research team has also hand-picked tens of thousands of additional genetic variants linked to various conditions and traits in the scientific literature to analyze on our genotyping chip. As a result we can provide you with personal genetic information available only through 23andMe.

Genetics service 23andMe announced some new cash in the bank today with a $50 million raise from Yuri Milner, 23andMe CEO Anne Wojcicki, Google’s Sergey Brin (who also happens to be Wojcicki’s husband), New Enterprise Associates, MPM Capital, and Google Ventures.

With today’s new funding also comes the reduction of the price of its genome analysis service to $99. This isn’t special holiday pricing (as 23andMe has run repeatedly in the past) the company tells me, but rather what its normal pricing will be from now on.

This move is overdue, at least as far as 23andMe’s business model is concerned. Just yesterday TechCrunch Conference Chair Susan Hobbs told me she was waiting for another $99 pricing deal to buy the Personal Genome Analysis product. Sure 23andMe has experimented with various pricing models, including subscription, since its founding in 2007, but had been at an official and prohibitive $299 price point until today. It’s also apparently been rigorously beta-testing various price points in the past couple of weeks, at some point experimenting with some lower than $99.

For comparison, the company’s original pricing began at $999 and offered subscribers just 14 health and trait reports versus today’s 244 reports, as well as genetic ancestry information. Natera, Counsyl and Pathway Genomics are also in the genomics space, but they work by offering their services through doctors rather than direct to consumer.

Since the company’s launch five years ago, it’s had 180K civilians profile their DNA, and representative Catherine Afarian tells us that, post-price drop and funding, its goal is to reach a million customers in 2013. This is a supremely ambitious goal considering it wants to turn an average user acquisition rate of 36K per year into one of 820K in one year alone.

But Afarian isn’t fazed and brings up how the company once sold out 20k in $99 account inventory on something called “DNA Day.” “Once we can offer the service at $99 it means the average American will buy in,” she said.

That $299 was too pricey, according to Hobbs, but $99 might be just right. She said the $99 price point, which yes, is less than an iPhone, was the main factor in her decision to buy in. “23andMe is more ‘nice-to-know’ information rather than ‘need-to-know’ information. It’s nice to know your ancestry. It’s more of a need to know that you are predisposed genetically for a type of cancer, so that you may take precautionary measures,” she said, implying that the data given by 23andMe isn’t necessarily vital medical information, or actionable when it is. While 23andMe can give you indicators about certain disease risks, it doesn’t close the loop, as in tell you what to do to prevent these diseases.

“Its [utility] depends on your genetic data,” said Afarian when I asked her about the usefulness of the product. “If you’ve got a Factor 5 that puts you at risk for clotting, you might want to invest in anti-clotting socks. [And] there’s always something about themselves that people didn’t know.”

Hobbs said eventually that she wouldn’t buy it, but only because she was looking into more exact lineage information for her little girl, and you need a Y chromosome in all DNA tests to show paternal lineage. Afarian also countered this hesitation, saying that what makes 23andMe unique is that it’s not only looking at just your Y or your mitochondrial DNA, but also your autosomal DNA, which does show some patrilineal information for females who lack that precious Y.

While still sort of a novelty, the potential for 23andMe goes beyond lineage and hopefully that extra $50 million will go further than keeping the price low and into research. The company hopes that a million users will result in a giant database of 23andWe genetic info that can be used to spot trends, like which genes mean a higher risk of diabetes/cancer, etc. Which is great if it happens but for now remains a pipe dream for 23andMe/We.

http://techcrunch.com/2012/12/11/23andnotme/

12/13/2012 @ 5:23PM |6,471 views

What Is 23andMe Really Selling: The Moral Quandary At The Center Of The Personalized Genomics Revolution

This week, 23andme, the personalized genomics company founded by Anne Wojcicki, wife of Google co-founder Sergey Brin, got an influx of investment cash ($50 million). According to their press release, they are using the money to bring the cost of their genetic test down to $99 (it was previously $299) which, they hope, will inspire the masses to get tested.

So should the masses indulge?

I prefer a quantified self approach to this question. At the heart of the quantified self-movement lies a very simple idea: metrics make us better. For devotees, this means “self-tracking,” using everything from the Nike fuel band to the Narcissism Personality Index to gather large quantities of personal data and—the bigger idea—use that data to improve performance.

If you consider that performance suffers when health suffers then a genetic test can been seen as a kind of metric used to improve performance. This strikes me as the best way to evaluate this idea and leads us to ask the same question about personalized genomics that the quantified self movement asks about every other metric: will it improve performance.

Arguments rage all over the place on this one, but the short answer is that SNP tests—which is the kind of DNA scan 23andme relies upon— don’t tell us all that much (yet).  They analyze a million genes out of three billion total and the impact those million play in long term-health outcomes is still in dispute. For example, the nature/nurture split is normally viewed at 30/70—meaning environmental factors play a far more significant role in long-term health outcomes than genetics.

Moreover, all of the performance metrics used by the quantified self movement are used to for behavior modification—to drive self-improvement. Personalized genomics isn’t there yet. As Stanford University’s Nobel Prize-winning RNA researcher Andy Fire once told me, “if someone off the street is looking for pointers on how to live a healthier life, there’s nothing these tests will tell you besides basic physician advice like ‘eat right, don’t smoke and get plenty of exercise.’”

And even with more well-regarded SNP tests, like the ones that examine the BRCA 1 and 2 markers for breast cancer—which  . NYU Langone Medical Center bioethicist Arthur Caplan explains it like this, “Say you test positive for a breast cancer disposition—then what are you going to do? The only preventative step you can take is to chop off your breasts.”

So if prevention is not available the only thing left is fear and anxiety. Unfortunately, in the past few decades, there have been hundreds of studies linking stress to everything from immunological disorders to heart disease to periodonitic troubles. So while finding out you may be at risk for Parkinson’s may make you feel informed, that knowledge isn’t going to stop you from developing the disease—but the resulting stress may contribute to a host of other complications.

This brings up a different question: if personalized genomics can’t yet help us much and could possibly hurt us—where’s the upside?

Turns out there’s a big upside: Citizen science. SNP tests are not yet viable because we need more info. 23andme talks about the “power of one million people,” meaning, if one million take these tests then the resulting genetic database could lead to big research breakthroughs and these could lead to all sorts of health/performance improvements.

This is what 23andme is really selling for $99 bucks a pop—a crowdsourced shot at unraveling a few more DNA mysteries.

And this also means that the question at the heart of the personalized genomics industry is not about metrics at all—it’s about morals: Should I risk my health for the greater good?

http://www.forbes.com/sites/stevenkotler/2012/12/13/what-is-23andme-really-selling-the-moral-quandary-at-the-center-of-the-personalized-genomics-revolution/

You can browse your data for all of the variants we test using the Browse Raw Data feature, or download your data here.

before you buy (59) »

What unexpected things might I learn?

How does 23andMe genotype my DNA?

Can I use the saliva collection kit for infants and toddlers?

getting started (20) »

When and how do I get my data?

How do I collect saliva samples?

How long will it take for my sample to reach the lab?

account/profile settings (20) »

Which Ancestry setting in My Profile should I choose?

How do I use Browse Raw Data?

What do the options under the “Account” link in the upper right-hand corner control?

product features (145) »

I know that a particular person is my relative. What’s the probability that we share a sufficient amount of DNA to be detected by Relative Finder?

What is the average percent DNA shared for different types of cousins?

How does Relative Finder estimate the Predicted Relationship?

research initiatives (8) »

What do I get in return for taking surveys?

What is your research goal?

What is 23andMe Research?

https://customercare.23andme.com/categories/20021003-faqs

https://customercare.23andme.com/home

REFERENCES

http://www.foundationmedicine.com/diagnostics-publications.php

http://www.coriell.org/media-center/publications

Http://www.coriell.org/assets/pdfs/gronowski_etal_coriellinstitute_clinicalchemistry2011_humantissuesinresearch.pdf

http://scholar.google.com/scholar?start=10&q=Gene+Mutation+Aberration+%26+Analysis+of+Gene+Abnormalities&hl=en&as_sdt=0,22&as_vis=1

Read Full Post »

Reporter: Aviva Lev-Ari, PhD, RN

Cancer Diagnostics by Genomic Sequencing: ‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

How to Tailor Cancer Therapy to the particular Genetics of a patient’s Cancer

THIS IS A SERIES OF FOUR POINTS OF VIEW IN SUPPORT OF the Paradigm Shift in Human Genomics

‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

PRESENTED in the following FOUR PARTS. Recommended to be read in its entirety for completeness and arrival to the End Point of Present and Future Frontier of Research in Genomics

Part 1:

Research Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine

http://pharmaceuticalintelligence.com/2013/01/13/paradigm-shift-in-human-genomics-predictive-biomarkers-and-personalized-medicine-part-1/

Part 2:

LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment

http://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-drug-selection-in-cancer-personalized-treatment-part-2/

Part 3:

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research

http://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical-research-part-3/

Part 4:

The Consumer Market for Personal DNA Sequencing

http://pharmaceuticalintelligence.com/2013/01/13/consumer-market-for-personal-dna-sequencing-part-4/

 

Part 3:

Personalized Medicine: Institute Profile – Coriell Institute for Medical Research

Coriell Institute for Medical Research, founded in 1953 and based in Camden, New Jersey, is an independent non-profit research center dedicated to the study of the human genome. Expert staff and pioneering programs in the fields of personalized medicine, cell biology, cytogenetics, genotyping, and biobanking drive our mission.

The emerging field of personalized medicine draws upon a person’s genomic information to tailor treatments and prescription drug dosing to optimize health outcomes. The Coriell Personalized Medicine Collaborative® (CPMC®) research study is seeking to understand the usefulness of genetic risk and pharmacogenomics in clinical decision-making and healthcare management.

Coriell has a distinguished history in cell biology. We are building upon this expertise by playing an important role in induced pluripotent stem (iPS) cell research. Induced pluripotent stem cells are powerful cells which can be made from skin or blood cells, and they are revolutionizing the way human disease is studied and how drugs are developed. Skin cells from a patient diagnosed with heart disease are being genetically reprogrammed into stem cells, and then transformed into beating cardiac cells. Researchers can now examine the heart-diseased cells to better understand the progression of heart disease and develop treatments and cures. Drug efficacy and safety can also be tested in this laboratory environment, providing an efficient model of drug discovery that delivers drugs to patients sooner. This technology, called “disease in a dish,” offers researchers the potential to study the myriad of human diseases, including Alzheimer’s disease, muscular dystrophy, and diabetes.

In addition to pioneering cutting-edge research initiatives, Coriell offers custom research services – including cell culture, cytogenetic analyses, and molecular biology – to the scientific community. Furthermore, Coriell’s Genotyping and Microarray Center is one of the nation’s largest centers, with high-throughput DNA analysis, CLIA-certified genotyping platforms systems from Illumina and Affymetrix.

Essential to the Institute’s support of international scientific research is the Coriell Biobank. From this renowned cell bank, we manage and distribute the world’s most diverse collection of cell lines, DNA, and other biological resources. The Coriell Biobank provided support to the Human Genome Project, a worldwide program to map the entire human genome, and to the International HapMap Project, a project providing an efficient tool to identify disease-causing genes.

The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.

The Business Aspects of the Institute

  • Personalized Medicine

DNA, Genes, and SNPs

What is the CPMC Study?

CPMC Technology

CPMC FAQs

CPMC Advisors and Partners

Stem Cells

Induced Pluripotent Stem (iPS) Cells

iPS Cell Research at Coriell

Biobank Catalog

Working with Coriell

  • Research Services

Overview

Biobanking

Cell Culture

Cytogenetics

Genotyping & Microarray

Molecular Biology

Research Design & Expertise

Stem Cells

Quality at Coriell

  • BioBanking

Overview

What is a Biobank?

How Coriell Banks Cells

Biobank Technology

Biobank Catalog

Working with Coriell

http://www.coriell.org/

http://www.coriell.org/assets/pdfs/discover-winter2012.pdf

http://www.ccr.coriell.org/

http://www.coriell.org/about/coriell-faqs

 

What is the Coriell Institute of Medical Research?

Founded in 1953, Coriell Institute for Medical Research is an independent, non-profit research organization dedicated to the study of the human genome and to supporting national and international research by providing biomaterials from its renowned biobank.

How did the Coriell Institute start?

Lewis L. Coriell, MD, PhD, a virology researcher and pediatrician, recognized the need for scientific research that would translate into better patient care. After seeing how his research helped to bring the Salk vaccine to polio patients across our nation, Dr. Coriell founded the South Jersey Medical Research Foundation. It was renamed the Institute for Medical Research in 1966 to recognize its broader reach, and, in 1985, to honor Dr. Coriell’s retirement, his name was added. For a look at our history, visit our timeline.

http://www.coriell.org/about/our-history

About the Founder

“You set up an experiment to test the theory, and most of the time it’s not the way you thought it would be. But that’s the way you learn. You go from hypothesis to hypothesis. And it’s exciting because that’s the way we learn to treat, to diagnose, and to prevent illness.”

Lewis L. Coriell, MD, PhD
Virologist and Pediatrician
June 19, 1911 – June 19, 2001

Lewis L. Coriell was born in the farming community of Sciotoville, in southern Ohio. While he was still a young child, his family moved to Montana toward more promising agricultural opportunities. It has been written that “the aspects of character, personality, temperament, and intellect that marked Dr. Coriell’s exceptional professional life… can easily be traced to his Montana upbringing.”i

Education and Early Career

Beginning his academic journey at the University of Montana, Lewis Coriell completed undergraduate studies in biology and subsequently earned a master’s degree in bacteriology and immunology in 1936. That same year, he married fellow student Ester Lentz; they would remain by each other’s side for the next 60 years. The newlyweds moved to the University of Kansas so he could pursue doctoral studies in immunology. While there, Dr. Coriell published his first article on an aspect of science he would revolutionize: The storage of cells by freezing them. Lewis Coriell earned his doctorate in 1940 and was awarded his medical degree in 1942. The young researcher was drawn to the field of virology – the study of viruses as they evolve and infect. At this time, bacterial infections presented themselves most often in children. This combination led Dr. Coriell to seek out a residency in pediatrics. As none were immediately available, he chose a cardiology residency at Henry Ford Hospital in Detroit. MI. As it happens, the Coriells’ time in Detroit was brief.

By 1943, World War II was raging and Dr. Coriell was called to service with the United States Army Medical Command’s Biological Research Division at Fort Detrick, MD. It was here that his research in cell cultivation began. After the war, Dr. Coriell began his ideal pediatric residency under Dr. Joseph Stokes, Jr., physician-in-chief at Children’s Hospital of Philadelphia (CHOP).  To his delight, Dr. Stokes placed great emphasis on research and was instrumental in attracting federal funds to research childhood disease at his institution.  The ability to translate research into patient care inspired Dr. Coriell.  He saw how research was essential to the treatment of his patients suffering the devastating effects of viruses like small pox, mumps, and polio.

Adventures in Cell Culture

By the time Dr. Coriell arrived in Philadelphia, virologists knew they had to grow viruses in cell culture to prepare purified viruses for the manufacture of vaccines. However, contamination was rife in the laboratory and proving to be a major obstacle. At CHOP, along with his colleagues, Dr. Coriell perfected the technique to culture human tissue in a sterile host that does not produce its own antibodies. The ability to sustain living human cells in culture, and keep them from being contaminated, led to a key breakthrough in polio research – it enabled scientists to grow the polio virus and work toward the first vaccine.

Moving to Camden and Taking on Polio

By the early 1950’s, an acute infectious disease called polio was spreading from person to person very quickly across the United States, striking fear into citizens, costing children their lives and crippling those who survived. In 1949, Dr. Coriell arrived in Camden, NJ, as medical director of Camden Municipal Hospital, one of the country’s last infectious disease hospitals and home to the majority of the region’s polio patients. In 1951, Dr. Coriell was appointed field director of the Polio Prevention Study and directed the successful gamma globulin field trials.

By 1954, the Salk polio vaccine could be made in large quantities and was ready for human clinical trials. Based on his success shepherding the gamma globulin field trials, Dr. Coriell was chosen by the National Poliomyelitis Foundation to evaluate the Salk polio virus vaccine clinical trials in New Jersey, Pennsylvania, Maryland, and Virginia. The success of the evaluation program led to the release of the Salk vaccine on the national level. Before the trials began in 1955, approximately 20,000 new polio cases were being reported each year. By 1960, cases were reduced to 3,000 per year. By 1979, that number was just 10 each year. Recognizing his contribution, Dr. Coriell received the 1957 International Poliomyelitis Congress Presidential Medal. Soon after, he became chairman of the Committee on the Control of Infectious Diseases of the American Academy of Pediatrics which formulated the vaccination procedures for all children in this critical period.

In 1953, Dr. Coriell initiated a campaign to build the first non-profit academic medical research institute in South Jersey. Under his guidance, the Institute for Medical Research began research in cancer, human cytogenetics, infectious diseases, and methods to improve cell culture techniques. The history of the Institute’s accomplishments included Dr. Coriell’s foresight in calling for the establishment of a central tissue culture bank and cell registry to certify and maintain cell cultures. It began with a partnership with the National Institutes of Health to create the first standardized cell repository. Today, the Institute is home to the world’s most diverse collection of cell lines and DNA samples available to researchers.

Working with his colleague, Dr. Gary McGarrity, Dr. Coriell applied infection control technology – specifically laminar flow – to create the laminar flow hood that is vital to infection control in laboratories, operating rooms, and hospital rooms around the world.

Dr. Coriell’s pioneering techniques for characterizing, freezing, and storing non-contaminated cell cultures in liquid nitrogen constitute one of the greatest contributions to modern human genetics.

Retirement

Dr. Coriell retired in 1985. To honor the occasion, the institute he founded was renamed the Coriell Institute for Medical Research. He remained involved in several ways, as a member of the board and often speaking with groups about the Institute’s history. Following his retirement, Dr. Coriell was elected president of the prestigious College of Physicians of Philadelphia, the oldest medical society in America. Dr. Coriell is the only New Jersey physician to receive this honor.

Dr. Coriell, a pioneering researcher and physician, died on June 19, 2001, in Southern New Jersey. It was his 90th birthday.

A Legacy in Science

Dr. Coriell’s accomplishments in science are indeed many. Perhaps Dr. Coriell’s most enduring legacy was his generosity in knowledge and his ability to bring scientists together to explore research questions and collaborate on solutions. Several important names in science were drawn to join or spend time at the Institute; they included Warren W. Nichols, Ray Dutcher, Richard Mulivor, Etienne Lasfargues, Jesse Charney, Arthur Greene, Daniel Moore, and collaboration with Drs. Albert Levan and Joe Hin Tijo, who first discovered that humans have 46 chromosomes.

Dr. Coriell also created an institute that is a well-respected resident of the Greater Philadelphia region and known as a leader in research worldwide.

Coriell Today

Dr. Coriell’s vision is now our vision. Today, Coriell staff and scientists collaborate on scientific ideas and programs to improve human health.

The Coriell Personalized Medicine Collaborative® research study is studying the utility of using your genetic information to tailor treatments and medications for you. And building on Dr. Coriell’s innovations in cell biology, we are playing an important role in cutting-edge stem cell research to unlock the code of human disease, including Parkinson’s and heart disease. Coriell offers a range of custom research services that have long supported national and international science. In the field of biobanking, Coriell supports research all over the world from its renowned and diverse cell collections.

Our innovation today is a testament to Dr. Coriell’s pioneering past. More importantly, our innovation is a commitment to your future.

i O’Donnell, John. Coriell; The Coriell Institute for Medical Research and a Half Century of Science. Massachusetts: SHP, 2002.

Where is the Coriell Institute located?

Coriell is located at 403 Haddon Avenue, Camden, NJ 08103. For directions, click here
We recommend that you park at 3 Cooper Plaza, a parking garage associated with the hospital, located directly across the street from Coriell. There is also a second hospital parking lot located on Benson Street, which is a block from the Institute.

For what is the Coriell Institute known?

Coriell Institute is a leader in the emerging field of personalized medicine – often called genome-informed medicine – which is the practice of using genetic information to better understand a patient’s risk for disease and response to medications. The Coriell Personalized Medicine Collaborative is a research study designed to study the utility of genetic information in clinical decision-making and patient care.

Coriell is also playing an important role in exploring the promise of induced pluripotent stem (iPS) cell  biotechnologies. [Pluripotent refers to how cells can grow into many different types of cells.] We can take skin cells and reprogram them – essentially turn back time – to behave like a stem cell. These cells can then be triggered, using specific proteins, to become cardiac cells, neurons (brain cells), or insulin-producing pancreatic cells, amongst others. Over the years, Coriell has developed an extraordinary expertise in the culture of human cells, and much of the standard practices in cell culture were developed at Coriell. This includes the techniques for freezing and thawing cells, and sterile handling of cultures. As a result of our cell biology expertise, scientists from every major research center in the world draw upon the Coriell Cell Repositories, maintained in the world’s leading biobank, which contains cell lines and DNA representing approximately 650 diseases.

Who is on the Coriell Institute staff?

Coriell is home to approximately 120 scientific and operational staff. Michael Christman, PhD, is Coriell’s President and CEO; he is an expert in genomics and genetics.  Joseph L. Mintzer is Coriell’s Executive Vice President and COO and manages the fiscal and operational aspect of the institute. Meet the rest of the Coriell leadership team here.

Who is on the Coriell Institute Board of Trustees?

Coriell is guided by a diverse Board of Trustees that includes corporate, medical, financial, and philanthropic leaders. Chairman of the Coriell Board is Robert P. Kiep III. Learn more about the Coriell Board of Trustees here.

How is Coriell Institute funded?

Coriell Institute has an annual operating budget of $17 million, about $11 million of which comes from federally- and state-funded grants and contracts. Private and corporate philanthropy provides the seed money to initiate new programs in science at Coriell – science that has the opportunity to advance discoveries in research which may not be occurring at other research institutes.

How can I support the research mission of Coriell Institute?

While the majority of Coriell’s operating revenue is derived from federally- and state-funded grants and contracts, the Institute also relies on private, foundation, and corporate philanthropy. Your support can advance the emerging field of personalized medicine to improve the practice of medicine. Your support also allows Coriell to pursue and support research in adult stem cell biology and genomics seeking to unlock the code of human disease. 
There are many ways to give to Coriell: Outrights gifts, through your workplace giving programs, planned giving, volunteering your time and expertise, or attending or hosting a Coriell event. Visit our fund development page to learn more about how you can support scientific research.

How does Coriell Institute support international research?

The Coriell Cell Repositories offers essential research materials to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA. Since the first NIH-sponsored repository was established in 1964 – Coriell has distributed hundreds of thousands of cell lines and DNA samples to researchers in 64 countries. More than 7,000 peer-reviewed papers have been published citing almost 12,000 Coriell Repository samples.

What research services does Coriell Institute provide? 
Coriell offers several best-in-class custom research services.

Coriell’s Genotyping and Microarray Center – one of the nation’s largest centers and CLIA-certified in 48 states – is a high-capacity facility with high-throughput systems from Affymetrix and Illumina.

The Coriell Institute Cytogenetics Laboratory is a state-of-the-art facility that combines conventional and molecular cytogenetic analyses with copy number and loss of heterozygosity (LOH) analyses by microarray. The laboratory is equipped with a network of five Applied Spectral Imaging work-stations that are used to perform G-banded karyotyping, and Fluorescent In Situ Hybridization (FISH).

Coriell also offers many preparative and diagnostic nucleic acid and molecular biology services, all subject to extensive quality controls.

And, the Coriell biobank is regarded as the most diverse collection of cell lines and DNA available to the international research community.

Does Coriell Institute engage in gene therapy or stem cell clinical trials?

Coriell Institute does not pursue research using human embryonic stem cells, nor do we conduct clinical trials on stem cell technologies. If you are interested in gene therapy or stem cell-related clinical trials, please visit http://www.clinicaltrials.gov.

What education does Coriell offer?

Coriell offers a course in cell culture: Advanced biology coupled with the history, theory, and techniques of maintaining live cells in long-term culture is offered to students.

Coriell also invites a limited number of motivated students into the Institute to participate in a Summer Experience program to gain insight into the workings of an independent research institute

How can I stay informed on what is happening at Coriell Institute?

Sign up for our email updates and you’ll receive periodic research news, notable donations, and upcoming events. Visit our Media Center regularly to read the latest news articles and Coriell press releases.

How can I get a quick overview of Coriell Institute?

Read our Coriell Fast Facts for a basic introduction to the Institute. For more information, explore the About section of our website.

Are Coriell Institute scientists and staff available for speaking engagements?

As their schedules permit, Coriell’s scientific and operational staffs enjoy the opportunity to highlight the work occurring at Coriell. Many hold joint faculty appointments at our region’s universities and teach an array of topics from business management and healthcare policy to the science of cell culture and stem cell research.

Coriell also participates in several outreach programs each year, including science festivals and conferences. We also host tours of our laboratories for business and governmental leaders and middle school and high school students.

16. Is Coriell Institute affiliated with Cooper Medical School of Rowan University?
Yes; Coriell is looking forward to welcoming the new medical school and will be integral in teaching genetics and genomics to the next generation of healthcare providers.

Fig3a-200

The Power of Stem Cell Science

The promise of stem cell research lays in its application in understanding the progression of human disease, the ability to cure disease and reverse injury, and to better target therapies to optimize our health outcomes. Induced pluripotent stem (iPS) cell technology has the ability to revolutionize the way human disease is studied. Creating iPS cell lines from various rare and common disease states, as well as from various populations, will open the doors for pre-clinical research studies.

Fig3b-200

Let Our Expertise Make Your Research a Success

Coriell offers a range of custom research services that have long supported national and international science. Whether you are requesting a cell line for your research studies or submitting DNA samples for genotyping analysis, Coriell is committed to providing you with flexible, innovative, and results-oriented research services. Our laboratories are built to foster scientific collaboration, and your research will benefit from this collaborative environment.

Coriell’s Biobank and Cell Culture Laboratory have established the gold standard in the cryopreservation of biomaterials and the capacity to support varied research worldwide. The diverse collections of biological specimens managed by Coriell offer the scientific community the highest quality specimens, which are necessary for successful research endeavors. Since the first repository – a National Institutes of Health collection – was established at Coriell in 1964, hundreds of thousands of cell lines and DNA samples have been distributed to researchers in 64 countries; more than 7,000 peer-reviewed papers have been published citing almost 12,000 biospecimens from the Coriell Biobank.

Fig3c-200

Making Medicine Personalized for You

Our health is determined by many factors: the genetics we inherit; our innate personal traits of race, age and gender; our individual behavior; our family and community networks; and at the macro level, our economic, cultural, and environmental conditions. These factors are different for every person and will change over their lifespan. So too is a person’s experience with disease and how they respond to drugs or other medical interventions. Personalized medicine intends to make medical treatment as individual as the biology of one’s disease.

Personalized medicine has the potential to offer patients and their doctors several advantages, including:

The ability to make better informed clinical decisions.

A higher probability of desired health outcomes by using better-targeted therapies.

The reduced probability of adverse reactions from medications and treatments.

A focus on prevention and prediction of disease, rather than reaction to it.

Earlier disease intervention.

Reduced healthcare costs.

Fig3d-200

Preserving cells today for research tomorrow

Dr. Lewis Coriell’s pioneering techniques for characterizing, freezing, and storing cell cultures in liquid nitrogen constitute one of the greatest contributions to modern human research. Today, the Coriell Biobank is regarded as the most diverse collection of cell lines and DNA available to the international research community. In addition to these high-quality biospecimens, Coriell also maintains tissue, plasma, serum, urine, and cerebrospinal fluid.

Few organizations have the history of innovations in repository science that have been developed and implemented at Coriell. For nearly 60 years, Coriell has set the standard in biobanking services, including the experimental design, collection, processing, distribution, cryogenic preservation, and information management of human biomaterials used in research. By developing and maintaining biorepositories as national and international resources for the study of human diseases, aging, and neurological disease, Coriell is committed to providing the scientific community with well-characterized, cell cultures and DNA preparations, annotated with rich phenotypic data.

Catalog Collections

NIGMS Human Genetic Repository 
The Human Genetic Cell Repository, sponsored by the National Institute of General Medical Sciences, provides scientists around the world with resources for cell and genetic research. The samples include highly characterized cell lines and high quality DNA. Repository samples represent a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations.

NINDS Human Genetics DNA and Cell Line Repository 
The National Institute of Neurological Disorders and Stroke is committed to gene discovery, as a strategy for identifying the genetic causes and correlates of nervous system disorders. The NINDS Human Genetics DNA and Cell Line Repository banks samples from subjects with cerebrovascular disease, epilepsy, motor neuron disease, Parkinsonism, and Tourette Syndrome, as well as controls.

NIA Aging Cell Repository 
Sponsored by the National Institute on Aging (NIA), the AGING CELL REPOSITORY, is a resource facilitating cellular and molecular research studies on the mechanisms of aging and the degenerative processes associated with it. The cells in this resource have been collected over the past three decades using strict diagnostic criteria and banked under the highest quality standards of cell culture. Scientists use the highly-characterized, viable, and contaminant-free cell cultures from this collection for research on such diseases as Alzheimer disease, progeria, Parkinsonism, Werner syndrome, and Cockayne syndrome.

NHGRI Sample Repository for Human Genetic Research 
The National Human Genome Research Institute (NHGRI) led the National Institutes of Health’s (NIH) contribution to the International Human Genome Project, which had as its primary goal the sequencing of the human genome. This project was successfully completed in April 2003. Now, the NHGRI’s mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease.

American Diabetes Association, GENNID Study 
The purpose of the American Diabetes Association (ADA), GENNID Study (Genetics of non-insulin dependent diabetes mellitus, NIDDM) is to establish a national database and cell repository consisting of information and genetic material from families with well-documented NIDDM. The GENNID Study will provide investigators with the information and samples necessary to conduct genetic linkage studies and locate the genes for NIDDM.

The Autism Research Resource 
The State of New Jersey funded the initiation of a genetic resource to support the study of autism in families where more than one child is affected or where one child is affected and one demonstrates another significant and related developmental disorder. This resource now receives continuing support from the Coriell Institute for Medical Research. An open bank of anonymously collected materials documented by a detailed clinical diagnosis forms the basis of this growing database of information about the disease.

IPBIR Repository 
The purpose of the IPBIR – Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics.

HD Community BioRepository 
HD Community BioRepository is a secure, centralized repository that stores and distributes quality-controlled, reliable research reagents. Huntingtin DNAs are now available and antibodies, antigenic peptides, cell lines, and hybridomas will be added soon.

USIDNET Repository 
The USIDNET DNA and Cell Repository has been established as part of an NIH-funded program – the US Immunodeficiency Network (www.usidnet.org) – to provide a resource of DNA and functional lymphoid cells obtained from patients with various primary immunodeficiency diseases. These uncommon disorders include patients with defects in T cell, B cell and/or granulocyte function as well as patients with abnormalities in antibodies/immunoglobulins, complement and other host defense mechanisms.

CDC Cell and DNA Repository 
The Genetic Testing Reference Material Coordination Program of the Centers for Disease Control and Prevention (CDC) and the Coriell Institute for Medical Research announce the availability of samples derived from transformed cell lines for use in molecular genetic testing. The DNA samples prepared from these reference cell lines are available through the Coriell Cell Repositories. Diseases include cystic fibrosis (CF), 5′ 10′ methylenetetrahydrofolate reductase deficiency (MTHFR), HFE-associated hereditary hemochromatosis, Huntington disease (HD), fragile X syndrome, Muenke syndrome, connexin 26-associated deafness, and alpha-thalassemia.

Leiomyosarcoma Cell and DNA Repository 
The Leiomyosarcoma Cell and DNA Repository has been established with an award from the National Leiomyosarcoma Foundation. This foundation provides leadership in supporting research of Leiomyosarcoma, improving treatment outcomes of those affected by this disease as well as fostering awareness in the medical community and general public.

COHORT Project 
The Cooperative Huntington’s Observational Trial Repository has been established as a resource for the discovery of information related to Huntington’s disease and its causes, progressioin, treatments, and possible cures. This is a growing bank for DATA and SPECIMENS to accelerate research on Huntington’s disease.

YERKES Repository 
The Yerkes National Primate Research Center of Emory University is an international leader in biomedical and behavioral research. For more than seven decades, the Yerkes Research Center has been dedicated to advancing scientific understanding of primate biology, behavior, veterinary care and conservation, and to improving human health and well-being.

NEI-AREDS Genetic Repository 
The Age-Related Eye Disease Study was designed to learn about macular degeneration and cataract, two leading causes of vision loss in older adults. The study looked at how these two diseases progress and what their causes may be. In addition, the study tested certain vitamins and minerals to find out if they can help to prevent or slow these diseases. Participants in the study did not have to have either disease. (Enrollment was completed in January 1998.) Eleven medical centers in the United States took part in the study, and more than 4,700 people across the country were enrolled in AREDS. The study was supported by the National Eye Institute, part of the Federal government’s National Institutes of Health. The clinical trial portion of the study also received support from Bausch & Lomb Pharmaceuticals and was completed in October 2001. Learn about the results of the clinical trial on the National Eye Institute’s website: http://www.nei.nih.gov/amd/.

The Wistar Institute 
The Wistar Institute collection at Coriell contains cell lines that have been developed by Wistar scientists. These materials are offered for non-commercial research conducted by universities, government agencies and academic research centers. The Wistar Institute collection currently contains a group of hybridomas that produce monoclonal antibodies that are useful in influenza research and vaccine development. Melanoma cell lines, derived from patients with a wide range of disease ranging from mild dysplasia to advanced metastatic cancer, will be added shortly. More information on The Wistar Institute, its research and scientists can be found at www.wistar.org.

J. Craig Venter Institute Human Reference Genome (HuRef) 
The Human Reference Genetic Material Repository makes available DNA from a single individual, J. Craig Venter, whose genome has been sequenced and assembled. The DNA samples are prepared from a lymphoblastoid cell line established at Coriell Cell Repositories from a sample of peripheral blood. The DNA samples are available in 50 microgram aliquots. The lymphoblastoid cell line is not available for distribution..

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LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

Curator:  Aviva Lev-Ari, PhD, RN

 

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WordCloud Image Produced by Adam Tubman

 

Cancer Diagnostics by Genomic Sequencing: ‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

How to Tailor Cancer Therapy to the particular Genetics of a patient’s Cancer

THIS IS A SERIES OF FOUR POINTS OF VIEW IN SUPPORT OF the Paradigm Shift in Human Genomics

‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

PRESENTED in the following FOUR PARTS. Recommended to be read in its entirety for completeness and arrival to the End Point of Present and Future Frontier of Research in Genomics

Part 1:

Research Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine

http://pharmaceuticalintelligence.com/2013/01/13/paradigm-shift-in-human-genomics-predictive-biomarkers-and-personalized-medicine-part-1/

Part 2:

LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment

http://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-drug-selection-in-cancer-personalized-treatment-part-2/

Part 3:

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research

http://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical-research-part-3/

Part 4:

The Consumer Market for Personal DNA Sequencing

http://pharmaceuticalintelligence.com/2013/01/13/consumer-market-for-personal-dna-sequencing-part-4/

 

 

Part 2:

LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment

 

  • Foundation Medicine, a Cambridge, Mass.-based company that sells a $5,800 diagnostic test that uses DNA sequencing to help doctors guess which cancer drugs would be helpful in fighting a particular patient’s tumor.

CAMBRIDGE, Mass., January 8, 2013 – Foundation Medicine, Inc. today announced an expansion of its Series B financing, raising an additional $13.5 million and bringing the total raised in the round to $56 million. The new investors include Bill Gates, Evan Jones and Yuri Milner.

“Advances in understanding the human genome are having a dramatic impact on almost every area of medicine,” said Bill Gates. “Foundation Medicine’s approach in harnessing the power of genomic data to improve care for cancer patients could represent an extremely important step forward in improving routine cancer care. I’m happy to be supporting this quite promising approach.”

http://www.foundationmedicine.com/pdf/news-releases/2013_01_08_FMI_Series_B_Ext_FINAL.pdf

Foundation, which previously listed Kleiner Perkins Caulfield & Byers and Google Ventures, raised $13.5 million in the series B round in which Gates participated, bringing its total take to $56 million. The other investors were Facebook billionaire Yuri Milner, who also recently invested in the personal genomics company 23andMe, and Evan Jones, the diagnostics industry legend who founded DiGene, which was sold to Qiagen for $1.6 billion in 2007. Jones will also join Foundation’s board.

http://www.forbes.com/sites/matthewherper/2013/01/08/bill-gates-invests-in-cancer-dna-sequencing-firm/

It now costs as little as $1,000 to get a fairly accurate readout of the 6 billion letters of DNA code for any single person.

In cancer, the approach right now is usually not to sequence all a patient’s DNA or that of his tumor, but instead to focus on particular genetic mutations in the tumor that might provide clues as to what medicines to try. Major cancer centers are using this approach with patients for whom it’s not obvious which medicine represents the best bet. Foundation’s approach has been to provide that kind of testing to a larger audience. To do so, it uses the DNA sequencing machines made by Illumina and other companies.

“What we want to do is take this testing to the community practices to treat patients where they live,” Michael Pellini, Foundation’s chief executive, 2011.

There is some evidence backing up that test. In a study conducted with the Dana-Farber Cancer Institute and published in Nature Medicine, found that more than half of patients with lung and colon cancer might benefit from the test.  from high-speed tests that detect DNA flaws doctors can target with existing medicines, a study found.

Researchers used a gene test made by closely held Foundation Medicine Inc. to sequence 145 cancer-associated genes in 40 colon tumor samples and 24 lung tumors.

They found that

53 percent of colon tumors and

71 percent of lung tumors

had mutations that may be attacked with cancer medicines on the market or in human trials, according to the study published in Nature Medicine. In some cases, the results revealed what drugs wouldn’t work against the tumors.

The study from researchers at Foundation Medicine and the Dana-Farber Cancer Institute in Boston, shows the value of using DNA sequencing machines to optimize treatment by matching drugs against specific gene abnormalities inside a patient’s tumor, said Pasi Janne, a study co-author.

Finding Gene Abnormalities

Maureen Cronin, a study co-author and molecular pharmacologist at Cambridge, Massachusetts-based Foundation Medicine, said her company was finding new gene abnormalities at a much higher rate than they expected as it performs DNA scans on tumors.

“We expected to find new things, but not at the frequency we are finding them,” she said in a telephone interview. The results “are very surprising.

The study also suggests cancer researchers may need to rethink the way they classify and treat the disease, Cronin said. The particular genetic abnormality inside tumor DNA may matter as much as what organ the tumor came from, she said.

Pfizer is aware of the new lung cancer gene finding and “believes the data are interesting,” said Jenifer Antonacci, a company spokeswoman, in an e-mail.

Laura Woodin, a spokeswoman for London-based AstraZeneca, said the company “is constantly alert to new developments and research in the science of oncology and we review relevant, peer reviewed studies for what they might mean for patients and drug development.”

Foundation Medicine performs a $5,800 test that takes tumor samples and sequences DNA from 200 genes relevant to cancer. It is funded with $33.5 million in venture capital from Third Rock Ventures, Kleiner Perkins Caufield & Byers and Google Ventures, according to its website. $56 Millions on January 8, 2013.

It is difficult to analyze DNA data, Foundation’s test is anything but a full genome, it’s a $6,000 .02% of the genome, showing how much of the problem of using genetic information will need to coming from solving computational and analytical problems — exactly the kind of thing that Bill Gates has always been interested in both at Microsoft and in his work getting lifesaving vaccines to children all around the world.

http://www.bloomberg.com/news/2012-02-12/high-speed-dna-scans-help-most-lung-cancer-patients-study-finds.html

Physicians need to incorporate the latest molecular diagnostic tests to help guide treatment of cancer patients due to the growing number of molecular subtypes that are understood across tumor types.

As more targeted therapies are approved for new molecular subtypes, the number of tests that need to be performed on each patient to determine their subtype increases and very quickly exhausts the very small amount of tumor tissue that is available in routine, clinical samples

Importantly, as patients’ molecular subtypes are more broadly incorporated into physician treatment decisions, we continue to further our understanding of a pathway view of cancer. Patients with different tumor types can have same molecular subtype – often, these therapies are applicable across tumor types since they are targeting the same pathway.

Comprehensive cancer genome analysis to routine cancer care. The company’s initial clinical assay, FoundationOneTM, is a fully informative genomic profile to identify a patient’s individual molecular alterations and match them with relevant targeted therapies and clinical trials.

http://www.foundationmedicine.com/diagnostics.php

The DNA sequencing field has drawn increased interest from pharmaceutical makers focused on developing gene-targeted therapies. Roche Holding AG (ROG), the world’s biggest maker of cancer medicines, last month began a $5.7 billion hostile takeover offer for Illumina Inc., the maker of gene sequencing machines that Foundation Medicine uses in its tests.

  • Pfizer’s Sutent

The researchers also spotted a previously unknown genetic flaw in 2 percent of 561 lung tumors tested. The flaw activates a growth-boosting protein targeted by Pfizer Inc. (PFE)’s kidney- cancer drug Sutent, hinting that the treatment from the New York-based drugmaker may also work in these lung patients, said Janne. He wants to begin a trial of Sutent in lung-cancer patients with the gene change by year end, he said.

Lev-Ari, A. (2012N). Sunitinib (Sutent) brings Adult acute lymphoblastic leukemia (ALL) to Remission – RNA Sequencing – FLT3 Receptor Blockade

http://pharmaceuticalintelligence.com/2012/07/09/sunitinib-brings-adult-all-to-remission-rna-sequencing/

Pfizer’s Kidney Cancer Drug Sutent Effectively caused REMISSION to Adult Acute Lymphoblastic Leukemia (ALL)

http://pharmaceuticalintelligence.com/2012/07/10/pfizers-kidney-cancer-drug-sutent-effectively-caused-remission-to-adult-acute-lymphoblastic-leukemia-all/REMISSION to Adult Acute Lymphoblastic Leukemia (ALL)

REMISSION to Adult Acute Lymphoblastic Leukemia (ALL): Pfizer’s Sutent blocks FLT3 Gene Receptors

http://pharmaceuticalintelligence.com/?s=Pfizer

Researchers in Japan also reported finding the same new genetic change in a fraction of lung tumors, according to two other studies published today in Nature Medicine. Until the three new studies, the genetic change had never been seen in any cancer, said Dr. Pasi Janne.

The change fuses two unrelated genes together to form KIF5B-RET, turning on a growth-driving protein called RET that is usually not active in lung cells.

When Pasi Janne and his collaborators treated cells with the aberrant gene using Pfizer’s Sutent or AstraZeneca Plc (AZN)’s thyroid-cancer drug Caprelsa, the cells died. Both drugs block RET.

http://www.google.com/search?q=pasi+janne+lab&hl=en&tbo=u&tbm=isch&source=univ&sa=X&ei=GzXzUMCyHYSK0QGouoCoAw&ved=0CD8QsAQ&biw=1140&bih=731

Pasi Antero Janne, M.D.,Ph.D.

Harvard Catalyst Profiles

http://connects.catalyst.harvard.edu/profiles/profile/person/711

  1. Yuen HF, Abramczyk O, Montgomery G, Chan KK, Huang YH, Sasazuki T, Shirasawa S, Gopesh S, Chan KW, Fennell D, Janne P, El-Tanani M, Murray JT. Impact of oncogenic driver mutations on feedback between the PI3K and MEK pathways in cancer cells. Biosci Rep. 2012 Aug 1; 32(4):413-22.
    View in: PubMed
  2. Tanizaki J, Okamoto I, Takezawa K, Sakai K, Azuma K, Kuwata K, Yamaguchi H, Hatashita E, Nishio K, Janne PA, Nakagawa K. Combined effect of ALK and MEK inhibitors in EML4-ALK-positive non-small-cell lung cancer cells. Br J Cancer. 2012 Feb 14; 106(4):763-7.
    View in: PubMed
  3. Vogelzang NJ, Benowitz SI, Adams S, Aghajanian C, Chang SM, Dreyer ZE, Janne PA, Ko AH, Masters GA, Odenike O, Patel JD, Roth BJ, Samlowski WE, Seidman AD, Tap WD, Temel JS, Von Roenn JH, Kris MG. Clinical cancer advances 2011: annual report on progress against cancer from the american society of clinical oncology. J Clin Oncol. 2012 Jan 1; 30(1):88-109.
    View in: PubMed
  4. Yuen HF, Chan KK, Grills C, Murray JT, Platt-Higgins A, Eldin OS, O’Byrne K, Janne P, Fennell DA, Johnston PG, Rudland PS, El-Tanani M. Ran Is a Potential Therapeutic Target for Cancer Cells with Molecular Changes Associated with Activation of the PI3K/Akt/mTORC1 and Ras/MEK/ERK Pathways. Clin Cancer Res. 2012 Jan 15; 18(2):380-91.
    View in: PubMed
  5. Hammerman PS, Sos ML, Ramos AH, Xu C, Dutt A, Zhou W, Brace LE, Woods BA, Lin W, Zhang J, Deng X, Lim SM, Heynck S, Peifer M, Simard JR, Lawrence MS, Onofrio RC, Salvesen HB, Seidel D, Zander T, Heuckmann JM, Soltermann A, Moch H, Koker M, Leenders F, Gabler F, Querings S, Ansén S, Brambilla E, Brambilla C, Lorimier P, Brustugun OT, Helland A, Petersen I, Clement JH, Groen H, Timens W, Sietsma H, Stoelben E, Wolf J, Beer DG, Tsao MS, Hanna M, Hatton C, Eck MJ, Janne PA, Johnson BE, Winckler W, Greulich H, Bass AJ, Cho J, Rauh D, Gray NS, Wong KK, Haura EB, Thomas RK, Meyerson M. Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov. 2011 Jun; 1(1):78-89.
    View in: PubMed
  6. Weisberg E, Choi HG, Ray A, Barrett R, Zhang J, Sim T, Zhou W, Seeliger M, Cameron M, Azam M, Fletcher JA, Debiec-Rychter M, Mayeda M, Moreno D, Kung AL, Janne PA, Khosravi-Far R, Melo JV, Manley PW, Adamia S, Wu C, Gray N, Griffin JD. Discovery of a small-molecule type II inhibitor of wild-type and gatekeeper mutants of BCR-ABL, PDGFRalpha, Kit, and Src kinases: novel type II inhibitor of gatekeeper mutants. Blood. 2010 May 27; 115(21):4206-16.
    View in: PubMed
  7. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M. The landscape of somatic copy-number alteration across human cancers. Nature. 2010 Feb 18; 463(7283):899-905.
    View in: PubMed
  8. Qin W, Kozlowski P, Taillon BE, Bouffard P, Holmes AJ, Janne P, Camposano S, Thiele E, Franz D, Kwiatkowski DJ. Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex. Hum Genet. 2010 Mar; 127(5):573-82.
    View in: PubMed
  9. Rodig SJ, Mino-Kenudson M, Dacic S, Yeap BY, Shaw A, Barletta JA, Stubbs H, Law K, Lindeman N, Mark E, Janne PA, Lynch T, Johnson BE, Iafrate AJ, Chirieac LR. Unique clinicopathologic features characterize ALK-rearranged lung adenocarcinoma in the western population. Clin Cancer Res. 2009 Aug 15; 15(16):5216-23.
    View in: PubMed
  10. Lynch TJ, Blumenschein GR, Engelman JA, Espinoza-Delgado I, Govindan R, Hanke J, Hanna NH, Heymach JV, Hirsch FR, Janne PA, Lilenbaum RC, Natale RB, Riely GJ, Sequist LV, Shapiro GI, Shaw A, Shepherd FA, Socinski M, Sorensen AG, Wakelee HA, Weitzman A. Summary statement novel agents in the treatment of lung cancer: Fifth Cambridge Conference assessing opportunities for combination therapy. J Thorac Oncol. 2008 Jun; 3(6 Suppl 2):S107-12.
    View in: PubMed
     

Read Full Post »

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

Article ID #16: Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1. Published on 1/13/2013

WordCloud Image Produced by Adam Tubman

Cancer Diagnostics by Genomic Sequencing: ‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

How to Tailor Cancer Therapy to the particular Genetics of a patient’s Cancer

THIS IS A SERIES OF FOUR POINTS OF VIEW IN SUPPORT OF the Paradigm Shift in Human Genomics

‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

PRESENTED in the following FOUR PARTS. Recommended to be read in its entirety for completeness and arrival to the End Point of Present and Future Frontier of Research in Genomics

Part 1:

Research Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine

Part 2:

LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment

http://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-drug-selection-in-cancer-personalized-treatment-part-2/

Part 3:

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research

http://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical-research-part-3/

Part 4:

The Consumer Market for Personal DNA Sequencing

http://pharmaceuticalintelligence.com/2013/01/13/consumer-market-for-personal-dna-sequencing-part-4/

 

Part 1:

Research Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine

 

In Part 1, we will address the following FIVE DIRECTIONS in Genomics Research

  • ‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities
  • Sequencing DNA from individual cells vs “humans as a whole.” Sequencing DNA from individual cells is changing the way that researchers think of humans as a whole.
  • Promising Research Directions By Watson, 1/10/2013
  • Disruption of Cancer Metabolism targeted by Metabolic Gatekeeper
  • Molecular Analysis of the different Stages of  Cancer Progression for Targeting Therapy

First:

Predictive Biomarkers and Personalized Medicine

No to Sequencing Patient’s DNA, No to Sequencing Patient’s Tumor, Yes to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

 

MD Anderson Research

targeted agents matched with tumor molecular aberrations.

Molecular analysis

Patients whose tumors had an aberration were treated with matched targeted therapy, compared with those of consecutive patients who were not treated with matched targeted therapy

Results

40.2% – 1 or more aberration.

In 1 aberration , matched tx higher response rate  27% vs 5%

Longer time ot treatment failure  TTF 5.2 vs. 2.2

Longer survival  13.4 vs. 9 months

Pt. w/1 mutation (molecular aberrationMatched targeted therapy associated with longer TTF vs. prior systemic therapy 5.2 vs. 3.1

matched therapy was an independent factor predicting response superior to TTF

Conclusion

Not randomized study, and patients had diverse tumor types and a median of 5 prior therapies,  results suggest that identifying specific molecular abnormalities and choosing therapy based on these abnormalities is relevant in phase I clinical trials

Clin Cancer Res. 2012 Nov 15;18(22):6373-83. doi: 10.1158/1078-0432.CCR-12-1627. Epub 2012 Sep 10.

Personalized medicine in a phase I clinical trials program: the MD Anderson Cancer Center initiative.

Tsimberidou AM, Iskander NG, Hong DS, Wheler JJ, Falchook GS, Fu S, Piha-Paul S, Naing A, Janku F, Luthra R, Ye Y, Wen S, Berry D, Kurzrock R.

Source

Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. atsimber@mdanderson.org

http://www.ncbi.nlm.nih.gov/pubmed?term=22966018

 

Opinion by Dr. Pierluigi Scalia, 1/11/2013.

The fact of using nanotechnology in order to target and treat abnormal cancer cells and tissues adds a powerful weapon towards eradicating the disease in the foreseeable future. However, focusing on weapons when we still have not found a reliable way to build that personalized “shooting target” (Cancer Fingerprinting) still constitutes, in my opinion, the single most relevant barrier to the adoption of Personalized treatments.

http://pharmaceuticalintelligence.com/2013/01/09/nanotechnology-personalized-medicine-and-dna-sequencing/

Ritu Saxena’s interview

http://pharmaceuticalintelligence.com/2013/01/07/personalized-medicine-gearing-up-to-tackle-cancer/

Other studies supporting this perspective

 

p53 gene deletion predicts for poor survival and non-response to therapy with purine analogs in chronic B-cell leukemias

 

Chromosome aberrations in solid tumors

 

Chromosome aberrations in B-cell chronic lymphocytic leukemia: reassessment based on molecular cytogenetic analysis

 

Multivariate analysis of prognostic factors in CLL: clinical stage, IGVH gene mutational status, and loss or mutation of the p53 gene are independent prognostic factors

 

Clonal analysis of delayed karyotypic abnormalities and gene mutations in radiation-induced genetic instability.

 

Comprehensive genetic characterization of CLL: a study on 506 cases analysed with chromosome banding analysis, interphase FISH, IgVH status and …

 

Detection of aberrations of the p53 alleles and the gene transcript in human tumor cell lines by single-strand conformation polymorphism analysis

 

Genetic aberrations detected by comparative genomic hybridization are associated with clinical outcome in renal cell carcinoma

 

VH mutation status, CD38 expression level, genomic aberrations, and survival in chronic lymphocytic leukemia

 

Microarray gene expression profiling of B-cell chronic lymphocytic leukemia subgroups defined by genomic aberrations and VH mutation status

 

… nucleophosmin (NPM1) predicts favorable prognosis in younger adults with acute myeloid leukemia and normal cytogenetics: interaction with other gene mutations

 

Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations

[DOC] Pax 6 Gene Research and the Pancreas

 

Molecular analysis of the cyclin-dependent kinase inhibitor gene p27/Kip1 in human malignancies

Molecular genetic analysis of oligodendroglial tumors shows preferential allelic deletions on 19q and 1p.

Cytogenetic analysis of soft tissue sarcomas: recurrent chromosome abnormalities in malignant peripheral nerve sheath tumors (MPNST)

Radiation-induced genomic instability: delayed cytogenetic aberrations and apoptosis in primary human bone marrow cells

SOURCES

Search:

Gene Mutation Aberration & Analysis of Gene Abnormalities

http://scholar.google.com/scholar?start=20&q=Gene+Mutation+Aberration+%26+Analysis+of+Gene+Abnormalities&hl=en&as_sdt=0,22&as_vis=1

Second:

Sequencing DNA from individual cells vs “humans as a whole.”

Sequencing DNA from individual cells is changing the way that researchers think of humans as a whole.

The ability to sequence single cells meant that researchers could take another approach. Working with a team at the Chinese sequencing powerhouse BGI, Auton sequenced nearly 200 sperm cells and was able to estimate the recombination rate for the man who had donated them. The work is not yet published, but Auton says that the group found an average of 24.5 recombination events per sperm cell, which is in line with estimates from indirect experiments2. Stephen Quake, a bioengineer at Stanford University in California, has performed similar experiments in 100 sperm cells and identified several places in the genome in which recombination is more likely to occur. The location of these recombination ‘hotspots’ could help population biologists to map the position of genetic variants associated with disease.

Quake also sequenced half a dozen of those 100 sperm in greater depth, and was able to determine the rate at which new mutations arise: about 30 mutations per billion bases per generation3, which is slightly higher than what others have found. “It’s basically the population biology of a sperm sample,” Quake says, and it will allow researchers to study meiosis and recombination in greater detail.

Fig1a

SOURCES:

http://www.nature.com/news/genomics-the-single-life-1.11710#/genome

Nature 491, 27–29 (01 November 2012) doi:10.1038/491027a

http://pharmaceuticalintelligence.com/2012/11/05/every-sperm-is-sacred-sequencing-dna-from-individual-cells-vs-humans-as-a-whole/

 

Third:

Promising Research Directions By Watson, 1/10/2013

The main reason drugs that target genetic glitches are not cures is that cancer cells have a work-around. If one biochemical pathway to growth and proliferation is blocked by a drug — the cancer cells activate a different, equally effective pathway.

Watson advocates a different approach: targeting features that all cancer cells, especially those in metastatic cancers, have in common.

A protein in cells called Myc. It controls more than 1,000 other molecules inside cells, including many involved in cancer. Studies suggest that turning off Myc causes cancer cells to self-destruct in a process called apoptosis.

cancer biologist Hans-Guido Wendel of Sloan-Kettering. “Blocking production of Myc is an interesting line of investigation. I think there’s promise in that.”

Personalized medicine” that targets a patient’s specific cancer-causing mutation

Watson wrote, may be “the inherently conservative nature of today’s cancer research establishments.”

http://pharmaceuticalintelligence.com/2013/01/09/the-cancer-establishments-examined-by-james-watson-co-discover-of-dna-wcrick-41953/

 

Opinion by Dr. Stephen Willliams, 1/11/2013

Kudos to both Watson and Weinstein for stating we really need to delve into tumor biology to determine functional pathways (like metabolism) which are a common feature of the malignant state ( also see my posting on differentiation therapy).

http://pharmaceuticalintelligence.com/2013/01/09/the-cancer-establishments-examined-by-james-watson-co-discover-of-dna-wcrick-41953/

http://pharmaceuticalintelligence.com/2013/01/03/differentiation-therapy-epigenetics-tackles-solid-tumors/

Fourth:

Disruption of Cancer Metabolism targeted by Metabolic Gatekeeper

Fig2a

Figure’s SOURCE:

Figure brought to my attention by Dr. Tilda Barlyia, 1/10/2013

http://blogs.nature.com/spoonful/2012/12/metabolic-gatekeeper-provides-new-target-for-disrupting-cancer-metabolism.html

Author: Yevgeniy Grigoryev

In the 1920s, the German physiologist Otto Warburgproposed that cancer cells generate energy in ways that are distinct from normal cells. Healthy cells mainly metabolize sugar via respiration in the mitochondria, switching only to glycolysis in the cytoplasm when oxygen levels are low. In contrast, cancer cells rely on glycolysis all the time, even under oxygen-rich scenarios. This shift in how energy is produced—the so-called ‘Warburg effect’, as the observation came to be known—is now recognized as a primary driver of tumor formation, but a mechanistic explanation for the phenomenon has remained elusive.

Now, researchers have implicated a chromatin regulator known as SIRT6 as a key mediator of the switch to glycolysis in cancer cells, a finding that could lead to new therapeutic modalities. “This work is very significant for the cancer field,” says Andrei Seluanov, a cancer biologist at the University of Rochester in New York State who studies SIRT6 but was not involved in the latest study. “It establishes the role ofSIRT6 as a tumor suppressor and shows that SIRT6 loss leads to tumor formation in mice and humans.”

SIRT6 encodes one of seven mammalian proteins called sirtuins, a group of histone deacetylases that play a role in regulating metabolism, lifespan and aging. SIRT1—which is activated by resveratrol, a molecule found in the skin of red grapes—is perhaps the best known sirtuin, but several of the others are now the focus of active investigation as therapeutic targets for a range of conditions, from metabolic syndrome tocancer. Just last month, for example, a paper in Nature Medicine demonstrated that SIRT6 plays an important role in heart disease.

Six years ago, a team led by Raul Mostoslavsky, a molecular biologist at the Massachusetts General Hospital Cancer Center in Boston, first showed that SIRT6 protects mice from DNA damage and had anti-aging properties. In 2010, the same team established SIRT6 as a critical regulator of glycolysis. Now,reporting today in Cell, Mostoslavsky and his colleagues have shown that SIRT6 function is lost in cancer cells—thus, definitively establishing SIRT6 as a potent tumor suppressor.

In the latest study, the researchers showed that mouse embryonic cells genetically engineered to lackSIRT6 proliferated much faster than normal cells, growing from 5,000 cells to 200,000 cells in three days. In contrast, SIRT6-expressiong cells grew at less than half that rate over the same time period. When injected into adult mice, these SIRT6-deficient cells also rapidly formed tumors, but this tumor growth was reversed when the scientists put SIRT6 back into the cells.

“Our study provides a proof-of-concept that inhibiting glycolysis in SIRT6-deficient cells and tumors could provide a potential therapeutic approach to combat cancer,” says Mostoslavsky. “Additionally, SIRT6 may be a valuable prognostic biomarker for cancer detection.”

Currently, there are no approved anti-glycolytic drugs against cancer. However, the latest findings indicate that pharmacologically elevating SIRT6 levels might help keep tumor growth at bay. And there’s preliminary data to suggest that the work will translate from the bench to the clinic: looking at a range of cancers from human patients, Mostoslavsky’s team showed that the higher the level of SIRT6 the better the prognosis and the longer the survival times.

SOURCE:

Fifth:

Molecular Analysis of the different Stages of  Cancer Progression: The Example of Breast Cancer 

Fig2b

Figure’s SOURCE:

The molecular pathology of breast cancer progression

Alessandro Bombonati1 and Dennis C Sgroi1,2* Journal of Pathology, J Pathol 2011; 223: 307–317

(wileyonlinelibrary.com) DOI: 10.1002/path.2808

http://onlinelibrary.wiley.com/store/10.1002/path.2808/asset/2808_ftp.pdf;jsessionid=26C2C424E6948A5FAF3CBADBA385184A.d02t04v=1&t=hi26qzd4&s=a8a4aadb3fc6d448080c0ef3c67415b8277145aa

Post by Dr. Tilda Barlyia and Comments on   “The Molecular Pathology of Breast Cancer Progression”

http://pharmaceuticalintelligence.com/2013/01/10/the-molecular-pathology-of-breast-cancer-progression/

Conclusion

The Paradigm Shift in Human Genomics will follow the following FIVE DIRECTIONS:

  • No to Sequencing Patient’s DNA, No to Sequencing Patient’s Tumor, Yes to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities
  • Sequencing DNA from individual cells vs “humans as a whole.” Sequencing DNA from individual cells is changing the way that researchers think of humans as a whole.
  • Promising Research Directions By Watson, 1/10/2013
  • Disruption of Cancer Metabolism targeted by Metabolic Gatekeeper
  • Molecular Analysis of the different Stages of  Cancer Progression for Targeting Therapy

Read Full Post »

PCI Outcomes, Increased Ischemic Risk associated with Elevated Plasma Fibrinogen not Platelet Reactivity

Reporter: Aviva Lev-Ari, PhD, RN

Article ID #13: PCI Outcomes, Increased Ischemic Risk associated with Elevated Plasma Fibrinogen not Platelet Reactivity. Published on 1/10/2013

WordCloud Image Produced by Adam Tubman

 

Q&A Session between Dr. Michael Ward and Dr. Larry Bernstein presented for in our Research Category on 

Interviews with Scientific Leaders

Primary research:

Ang L, et al “Elevated plasma fibrinogen rather than residual platelet reactivity after clopidogrel pre-treatment is associated with an increased ischemic risk during elective percutaneous coronary intervention” J Am Coll Cardiol2013; 61: 23-34.

 

Question by DR. MICHAEL WARD

How ironic that an old diagnostic parameter should
reappear in the limelight of diagnostic predictors.

Of course, decades ago, doctors asked for “sed rates”, seeking to know if red cells, thought to be bound to fibrinogen, settled faster in a patient compared to a control subject’s blood. Fibrinogen has always been a diagnostic number in evaluating inflammatory results.

However, the diagnostic world, like the worlds of pharmaceuticals, medical devices, biologics, and other industries, always seek the ‘new kid on the block’ to differentiate themselves from the rest of the pack in the
marketplace.

So there was a binge (and still is) to seek new and exotic blood proteins that are surrogate markers for specific diagnoses or prognoses.

That is the irony, that in this case at least, fibrinogen has come full circle. Biology works in mysterious ways.

Answer by Dr. Larry Bernstein, MD, FCAP

Dear Dr. M.  Ward:

Doctors asked for “sed rates”, seeking to know if red cells, thought to be bound to fibrinogen, settled faster in a patient compared to a control
subject’s blood. Fibrinogen has always been a diagnostic number in evaluating inflammatory results.

You are quite right that physicians used “sed rates” as a measure of inflammation, and more in Lupus Erythematosis, Rheumatoid Arthritis, Nephritides, Systemic Sclerosis, and so forth.  The “sed rate” was not a part of the thinking about CVD, and PCI didn’t exist.  Recently, MI post-PCI has been defined as a type (NSTEMI?).

Yes. In principle, the sed rate is related to fibrinogen and red-cell aggregation.  I am not prepared to accept that a platelet count over 400,000 would make no contribution, even if many of the PCI related infarcts are within a range of 150-300,000.  I don’t know how much power there is in the discussion.  The role of tissue factor (plaque), and of platelets in hemostasis is undeniable.

The industry does look for every opportunity to seize on promising biomarkers.  The coagulation assays developed at Dade-Behring (Dade, Dupont Division; then Dade) were far better and more explanatory that the “sed rate”.  The sed rate measurement requires that you set up graduated tubes to watch the rate of sedimentation.  It is not a walkaway procedure.  Industry has been so good at introducing automation that led to high volume efficiency, that this led to the only part of hospital operations that had good accounting measures.  The long trip to reducing personnel, but of course the profiles were a piece of cake.  I continually reorganized to carve out services for immunology and toxicology, which took longer to get automated.

The only use for sed rate now is for Temporal Thrombosis (?).

In the early days Yale NH Hospital had some 5 Perkin Elmer HPLCs to measure calcium.  Electrophoretic separation of isoenzymes was not helpful for managing patients.  The procedure was run batchwise once a day.  I was the first in CT to be running the immunoassay three times a day on the Roche COBAS Bio CFA., and Dupont put it on the ‘aca’.  A med tech could run it at 3 am  at Detroit Receiving, Bellevue, or Cook County, when the phone didn’t stop ringing for STAT results.

Physicians had expectations too.  So we had the progression from AST, LDH, and CK to isoenzyme MBCK, and then there were the cancer biomarkers – CEA, CA-125, PSA, with much to be discussed.

 

Q&A is derived from the following Article in

MedPage Today

Published: January 07, 2013

Fibrinogen Level Tied to Poorer PCI Outcomes

By Todd Neale, Senior Staff Writer, MedPage Today

Published: January 07, 2013

Reviewed by Robert Jasmer, MD; Associate Clinical Professor of Medicine, University of California, San Francisco and Dorothy Caputo, MA, BSN, RN, Nurse Planner

An elevated serum fibrinogen level predicted worse short-term ischemic outcomes among patients undergoing elective percutaneous coronary intervention after pretreatment with clopidogrel, researchers found.

Significantly higher levels of fibrinogen were seen in patients with periprocedural myocardial infarction (MI) defined by either creatine kinase-myocardial band (CK-MB) or troponin (P<0.02 for both), according to Ehtisham Mahmud, MD, of the University of California, San Diego, and colleagues.

Those relationships remained consistent after adjustment for several factors, including platelet function, which was not itself associated with periprocedural MI, the researchers reported in the Jan. 8 issue of the Journal of the American College of Cardiology.

“The results of the current study suggest that an elevated fibrinogen level…is related to significant platelet cross-linking and thrombus formation independent of residual P2Y12 receptor-mediated platelet activity during clopidogrel therapy,” they wrote.

Higher risk of ischemic cardiovascular events has been observed with both high platelet reactivity after thienopyridine treatment and elevated serum fibrinogen.

“As an acute phase reactant involved in the final common pathway of the coagulation cascade and essential component of platelet cross-linking in thrombus formation, fibrinogen possesses a clear biological mechanism for its adverse cardiovascular effects,” Mahmud and colleagues wrote.

In fact, high levels of serum fibrinogen have been shown to contribute to high platelet reactivity during clopidogrel treatment, resulting in uncertainty about whether insufficient platelet inhibition and elevated fibrinogen levels are independent or interactive risk factors for ischemic events.

To explore the issue, the researchers looked at data from 189 patients undergoing elective PCI who were pretreated with clopidogrel, defined as 75 mg daily for at least 7 days or a 600-mg bolus at least 12 hours before study enrollment. The mean age of the patients was 63.8 and most (74.1%) were male.

Nearly two-thirds (63%) had undergone a previous PCI, and 18% had undergone revascularization with coronary artery bypass grafting (CABG).

Baseline platelet function was measured using the VerifyNow P2Y12 assay. Markers of ischemic myocardial injury, including troponin and CK-MB, were measured every 8 hours after PCI until hospital discharge.

Periprocedural MI defined by troponin I or T occurred in 13.9% of patients. Those who had an MI had significantly higher levels of fibrinogen (363.1 versus 309.1 mg/dL, P=0.017).

The rate of CK-MB-defined periprocedural MI was 5.8%. Patients with that outcome also had elevated levels of fibrinogen (403.4 versus 313.5 mg/dL, P=0.007).

Both differences remained significant after multivariate adjustment that accounted for platelet function and other inflammatory markers.

The researchers found that a fibrinogen level of 345 mg/dL or higher — a cutoff identified as having optimal combined sensitivity and specificity for CK-MB-defined periprocedural MI — was associated with periprocedural MI defined by either troponin or CK-MB (P<0.04 for both).

Those relationships were stronger when systemic inflammation was low (C-reactive protein ≤0.5 mg/dL).

The platelet reactivity measurements were not associated with either definition of periprocedural MI, which is inconsistent with the findings from several smaller studies. The authors noted, however, that “the significance of these negative findings may be limited due to inadequate study power.”

In discussing the limitations of the study, the researchers pointed out that “the findings … do not provide insight into whether the relationship between high platelet reactivity and ischemic cardiovascular events demonstrated in previous studies is a direct one or mediated through the effect of serum fibrinogen.”

To get to the bottom of that, they wrote, “future studies relating platelet reactivity and adverse cardiac events should measure baseline fibrinogen.”

Mahmud has received clinical trial support from Accumetrics, Eli Lilly, and sanofi-aventis, and is on the speakers bureau for Medtronic. One of his co-authors is a consultant for Abbott Vascular, Boston Scientific, St. Jude Medical, Medtronic, and sanofi-aventis.

From the American Heart Association:

Todd Neale

Senior Staff Writer

Todd Neale, MedPage Today Staff Writer, got his start in journalism at Audubon Magazine and made a stop in directory publishing before landing at MedPage Today. He received a B.S. in biology from the University of Massachusetts Amherst and an M.A. in journalism from the Science, Health, and Environmental Reporting program at New York University.

SOURCE:

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Author, reporter: Tilda Barliya PhD

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Word Cloud By Danielle Smolyar

Breast cancer is the second most common cancer worldwide after lung cancer, the fifth most  common cause of cancer death, and the leading  cause of cancer death in women. the global burden of  breast cancer exceeds all other cancers and the incidence  rates of breast cancer are increasing (1,2).

The heterogeneity of breast cancers makes them both a fascinating and challenging solid tumor to diagnose and treat. Here is a great review of the molecular pathology of breast cancer progression (3).

The molecular pathology of breast cancer progression” by Alessandro Bombonati  and Dennis C Sgroi.

Breast cancer is the most frequent carcinoma in females and the second most common cause of cancer related mortality in women. Approximately 54 000 and 207 000 new cases of in situ and invasive breast carcinoma, respectively. Overall, breast cancer incidence rates have levelled off since 1990, with a decrease of 3.5%/year from 2001 to 2004.  Most notably, during this same time period, breast cancer mortality rates have declined 24%, with the largest impact among young women and women with estrogen receptor (ER)-positive disease.

The decline in breast cancer mortality has been attributed to the combination of early detection with screening programmes and the advent of more efficacious adjuvant progression have aided in the discovery of novel pathway-specific targeted therapeutics, and the emergence of such effective therapeutics is currently driving the need for molecular-based, ‘patient-tailored’ treatment planning.

Proposed models of human breast cancer progression

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Epidemiological and morp

hological observations led to the formulation of several linear models of breast cancer initiation, transformation and

progression. Figure 1

The ductal and lobular subtypes constitute the majority of all breast cancers worldwide, with the ductal subtype accounting for 40–75% of all diagnosed cases.

The classic model of breast cancer progression of the ductal type proposes thatneoplastic evolution initiates in normal epithelium (normal), progresses to flat epithelial atypia (FEA), advances to atypical ductalhyperplasia (ADH), evolves to ductal carcinoma in situ (DCIS) and culminates as invasive ductal carcinoma (IDC).

The model of lobular neoplasia proposes a multi-step progression from normal epithelium to atypicallobular hyperplasia, lobular carcinoma in situ (LCIS) and invasive lobular carcinoma (ILC).

The cell of origin of breast cancer: the clonal and stem cell hypotheses

The two leading models accounting for breast carcinogenesis are the sporadic clonal evolution model and the cancer stem cell (cSC) model. According to the sporadic clonal evolution hypothesis, any breast epithelial cell can be the target of random mutations. The cells with advantageous genetic and epigenetic alterations are selected over time to contribute to tumour progression. The third alternative cSC model postulates that only stem and progenitor cells (representing a small fraction of the tumor cells within the cancer) can initiate and maintain tumor progression. Figure 2.

Normal breast stem cells (nBSCs) are long-lived, tissue-resident cells capable of self-renewal activity and multi-lineage differentiation that can recapitulate the breast tubulolobular architecture that is composed of luminal and myoepithelial cells.

As normal breast cancer stem cells are long-time tissue residents, it has been proposed that such cells are candidates for accumulating genetic and epigenetic modifications. It has been further proposed that such molecular alterations result in deregulation of normal self-renewal, leading to the development of a cancer stem cell (cSC).

It is believed that the cSC undergoes asymmetrical division, maintaining the stem cell population while at the same time differentiating into committed progenitor(s) cells that give rise to the different breast cancer subtypes.

A second scenario, as it relates to breast cancer development, is one in which the cancer-initiating cells are derived from committed progenitor cells that spawn different breast cancer subtypes. Both scenarios are highly supported.

Molecular analysis of the different stages of breast cancer progression

An external file that holds a picture, illustration, etc.Object name is nihms247118f3.jpg Object name is nihms247118f3.jpg

Genomic and transcriptomic data in combination with morphological and immunohistochemical data stratify the majority of breast cancers into a “low-grade-like” molecular pathway and a “high-grade-like” molecular pathway. Figure 3. The low-grade-like pathway (left hand side) is characterized by recurrent chromosomal loss of 16q, gains of 1q, a low-grade-like gene expression signature, and the expression of estrogen and progesterone receptors (ER+ and PR+). The progression (vertical arrows) along this pathway (green rectangles) culminates with the formation of low and intermediate grade invasive ductal, (LG IDC and IG IDC) and invasive lobular carcinomas including both the classic (ILC) and the pleomorphic variant (pILC). The tumors arising from the low grade pathway are classified as luminal consisting of a continuum of gene expression frequently associated with the absence (luminal A) or presence of HER2 expression (luminal B). The vast majority of ILCs and pILCs and their precursors cluster together within the luminal subtype. The high grade-like gene expression molecular pathway (right hand side) is characterized by recurrent gain of 11q13 (+11q13), loss of 13q (13q−), expression of a high-grade-like gene expression signature, amplification of 17q12 (17q12AMP), and lack of estrogen and progesterone receptors expression (ER− and PR−). The progression along this pathway (red rectangles) includes intermediate and high grade ductal carcinomas that are stratified as HER2, or basal-like, depending on the expression/amplification of HER2. The molecular apocrine subtype, characterized by the lack of ER expression and presence of AR expression, arises from the high grade pathway. The model also depicts intra-pathway tumor grade progression (horizontal arrows).

Although the genomic and transcriptomic data presented in this review support the divergent model of breast cancer progression, the clinical experience indicates that tumors within each pathway are still fairly heterogeneous with respect to clinical outcome suggesting that even this advanced molecular progression scheme is oversimplified.

The future application of massively parallel sequencing technologies to the preinvasive stages of breast cancer will assist in assessing intratumoral heterogeneity during the transition from preinvasive to invasive breast cancer, and may assist in identifying early tumor initiating genetic events.

Summary:

Over the past decade the integration of numerous genomic and transcriptomic analyses of the various stages of breast cancer has generated multiple novel insights in the complex process of breast cancer progression.

  • First, human breast cancer appears to progress along two distinct molecular genetic pathways that strongly associate with tumor grade.
  • Second, in the epithelial and non-epithelial components of the tumor microenvironment, the greatest molecular alterations (at the gene expression level) occur prior to local invasion.
  • Third, in the epithelial compartment, no major additional gene expression changes occur between the preinvasive and invasive stages of breast cancer.
  • Fourth, the non-epithelial compartment of the tumor micromilieu undergoes dramatic epigenetic and gene expression alterations occur during the transition form preinvasive to invasive disease. Despite these significant advances, we have only begun to scratch the surface of this multifaceted biological process. With the advent of additional novel high-throughput genetic, epigenetic and proteomic technologies, it is anticipated that the next decade of breast cancer research will gain an equally paralleled appreciation for the complexity breast cancer progression. It is with great hope that knowledge gained from such studies will provide for more effective strategies to not only treat, but also prevent breast cancer.

Ref:

1. http://www.nature.com/nrclinonc/journal/v7/n12/pdf/nrclinonc.2010.192.pdf

2. Jemal, a. et al. CA Cancer J. Clin. 60, 277–300; 2010

3. Alessandro Bombonati and Dennis C Sgro. The molecular pathology of breast cancer progression. J Pathol 2011; 223: 307–317.

http://onlinelibrary.wiley.com/doi/10.1002/path.2808/pdf

http://pubmedcentralcanada.ca/pmcc/articles/PMC3069504/

4. Rodney C. Richie and John O. Swanson. Breast Cancer: A Review of the Literature. J Insur Med 2003;35:85–101.

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Reporter: Aviva Lev-Ari, PhD, RN

Scar Tissue In Damaged Hearts Reprogrammed By Gene Therapy Into Healthy Heart Muscle

Article Date: 08 Jan 2013 – 0:00 PST

A cocktail of three specific genes can reprogram cells in the scars caused by heart attacks into functioning muscle cells, and the addition of a gene that stimulates the growth of blood vessels enhances that effect, said researchers from Weill Cornell Medical College, Baylor College of Medicine and Stony Brook University Medical Center in a report that appears online in the Journal of the American Heart Association. 

“The idea of reprogramming scar tissue in the heart into functioning heart muscle was exciting,” said Dr. Todd K. Rosengart, chair of the Michael E. DeBakey Department of Surgery at BCM and the report’s corresponding author. “The theory is that if you have a big heart attack, your doctor can just inject these three genes into the scar tissue during surgery and change it back into heart muscle. However, in these animal studies, we found that even the effect is enhanced when combined with the VEGF gene.” 

“This experiment is a proof of principle,” said Dr. Ronald G. Crystal, chairman and professor of genetic medicine at Weill Cornell Medical College and a pioneer in gene therapy, who played an important role in the research. “Now we need to go further to understand the activity of these genes and determine if they are effective in even larger hearts.” 

During a heart attack, blood supply is cut off to the heart, resulting in the death of heart muscle. The damage leaves behind a scar and a much weakened heart. Eventually, most people who have had serious heart attacks will develop heart failure

Changing the scar into heart muscle would strengthen the heart. To accomplish this, during surgery, Rosengart and his colleagues transferred three forms of the vascular endothelial growth factor (VEGF) gene that enhances blood vessel growth or an inactive material (both attached to a gene vector) into the hearts of rats. Three weeks later, the rats received either Gata4, Mef 2c and Tbx5 (the cocktail of transcription factor genes called GMT) or an inactive material. (A transcription factor binds to specific DNA sequences and starts the process that translates the genetic information into a protein.) 

The GMT genes alone reduced the amount of scar tissue by half compared to animals that did not receive the genes, and there were more heart muscle cells in the animals that were treated with GMT. The hearts of animals that received GMT alone also worked better as defined by ejection fraction than those who had not received genes. (Ejection fraction refers to the percentage of blood that is pumped out of a filled ventricle or pumping chamber of the heart.) 

The hearts of the animals that had received both the GMT and the VEGF gene transfers had an ejection fraction four times greater than that of the animals that had received only the GMT transfer. 

Rosengart emphasizes that more work needs to be completed to show that the effect of the VEGF is real, but it has real promise as part of a new treatment for heart attack that would minimize heart damage. 

“We have shown both that GMT can effect change that enhances the activity of the heart and that the VEGF gene is effective in improving heart function even more,” said Dr. Crystal. 

The idea started with the notion of induced pluripotent stem cells – reprograming mature specialized cells into stem cells that are immature and can differentiate into different specific cells needed in the body. Dr. Shinya Yamanaka and Sir John B. Gurdon received the Nobel Prize in Medicine and Physiology for their work toward this goal this year. 

However, use of induced pluripotent stem cells has the potential to cause tumors. To get around that, researchers in Dallas and San Francisco used the GMT cocktail to reprogram the scar cells into cardiomyocytes (cells that become heart muscle) in the living animals. 

Now Rosengart and his colleagues have gone a step farther – encouraging the production of new blood vessels to provide circulation to the new cells.

REFERENCES:

Others who took part in this work include Megumi Mathison, Ronald Gersch, Ahmed Nasser, Sarit Lilo, Mallory Korman, Mitchell Fourman, Kenneth Shroyer, Jianchang Yang, Yupo Ma, all of Stony Brook University Medical Center and Neil Hackett of Weill Cornell Medical College.
Funding for this work came from the generosity of James and Lisa Cohen.
Weill Cornell Medical College

CITATIONS:

MLA

n.p. “Scar Tissue In Damaged Hearts Reprogrammed By Gene Therapy Into Healthy Heart Muscle.” Medical News Today. MediLexicon, Intl., 8 Jan. 2013. Web.
9 Jan. 2013. <http://www.medicalnewstoday.com/releases/254618.php>

APA

n.p. (2013, January 8). “Scar Tissue In Damaged Hearts Reprogrammed By Gene Therapy Into Healthy Heart Muscle.” Medical News Today. Retrieved from
http://www.medicalnewstoday.com/releases/254618.php.

SOURCE:

http://www.medicalnewstoday.com/releases/254618.php 

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Nanotechnology, personalized medicine and DNA sequencing

Author, reporter, Curator: Tilda Barliya PhD

Dr. Ritu Saxena’s exciting report on the fascinating work of Dr. Apostolia M. Tsimberidou “personalized medicine gearing up to tackle cancer”, inspired me to go back and review this topic and see how nanotechnology can be applied in personalized medicine.

To read the Dr. Saxena’s post, please see http://pharmaceuticalintelligence.com/2013/01/07/personalized-medicine-gearing-up-to-tackle-cancer/

It is based on an interview with Dr. A. M. Tsimberidou based on her paper:

Personalized medicine in a phase I clinical trials program: the MD Anderson Cancer Center initiative.

http://www.ncbi.nlm.nih.gov/pubmed?term=22966018

In March 2011 Nature Reviews issued a special issue features discussions of the advances, challenges and progress in the field of personalized cancer medicine by key opinion leaders who presented at the Worldwide Innovative Networking (WIN) symposium (**).

So what is personalized medicine?

Personalized medicine is a huge movement in the modern medical world. It aims to move away from the traditional practice of prescribing standard doses of standard drugs for a condition to every patient, and shifts the focus onto targeting the precise drug and dose required according to the patient’s physiology.

This is achieved by detecting and tracking molecular biomarkers, which indicate the presence and level of activity of a particular biological system in a patient’s body, whether inherent or foreign.

Another major part of the emerging field of personalized medicine is pharmacogenomics – analyzing the genetic makeup of the patient to determine whether a particular medication will be successful, or if it will have any adverse effects. (1). This is particularly important in cancer treatment, where the chemotherapy drugs used can be very damaging to healthy cells as well as cancerous ones, and the exact genetics of the tumor cells can vary widely between patients, and even between locations in one patient’s body.

Personalized medicine involves:

  • Detection (DNA polymorphism, RNA and protein expression, metabolits, Lipids etc)
  • Diagnosis (imaging)
  • Prognosis and
  • Treatment (targeted-therapy)

Given the size symmetry, nanomaterials offer unprecedented sensitivity, capable of sensing  biological markers and processes at the single-molecule or  single-cell level either in vitro or in vivo.  Techniques are being developed for high-throughput DNA sequencing using nanopores, to obtain genetic information from a patient so that targeted medication can be selected as rapidly as possible.

Cancer, a very complex disease, is propagated by various types of molecular aberrations which drive the development and progression of malignancies. Large-scale screenings of multiple types of molecular aberrations (e.g., mutations, copy number variations, DNA methylations, gene expressions) become increasingly important in the prognosis and study of cancer. Consequently, a computational model integrating multiple types of information is essential for the analysis of the comprehensive data.

One of the greatest promises of near-term nanotechnoloogy is cheaper DNA sequencing to speed the development of personalized medicine. (3)

Nanotechnology and DNA sequencing

Tumors are known to be highly heterogenetic, due to the many acquired aberration in the cancer cells. Therefore,  there are not only genetic differences between different patients, but also genetic differences within the same patient; for example from different locations in the same patient, that can greatly affect the success of a therapy.  Therefore, sensitive and extensive yet inexpensive whole-genome sequencing is of major medical need to enable the application personalized medicine.  A review of the potential of this emerging nanotechnology “Nanopore sensors for nucleic acid analysis ” was published recently in Nature Nanotechnology (4).

The growing need for cheaper and faster genome sequencing has prompted the development of new technologies that surpass conventional Sanger chain-termination methods in terms of speed and cost.  These second- and third-generation sequencing  technologies — inspired by the $1,000 genome challenge proposed by the National Institutes of Health in 2004 (ref. 5) — are expected to revolutionize genomic medicine. Nanopore sensors are one of a number of DNA sequencing technologies that are currently poised to meet this challenge.

Nanopore Sequencing:

Nanopore-based sensing is attractive for DNA sequencing applications because it is a

  • label-free,
  • amplification-free,
  • single-molecule
  • requires low reagent volumes

approach that can be scaled for high-throughput DNA analysis.

This approach can be scaled up for high-throughput DNA analysis, it typically requires low reagent volumes, benefits from
relatively low cost and supports long read lengths, so it could potentially enable de novo sequencing and long-range haplotype mapping. Although, nanopore technology is not conceptually new and raised many skeptical opinions it has made major progress in the past few years and are thus worth sharing.

The principle of nanopore sensing is analogous to that of a Coulter counter. A nanoscale aperture (the nanopore) is formed in an insulating membrane separating two chambers filled with conductive electrolyte. Charged molecules (A,G,C,T) are driven through the pore under an applied electric potential (a process known as electrophoresis), thereby modulating the ionic current through the nanopore. This current reveals useful information about the structure and dynamic motion of the molecule.

Here’s an example for  a nanopore-based sequencing device is a Graphene- chip that is used as trans-electrode membrane (5).

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Electrical measurements on graphene membranes in which a single nanopore has been drilled show that the membrane’s effective insulating thickness is less than one nanometer. This small effective thickness makes graphene an ideal substrate for very high-resolution, high throughput nanopore-based single molecule detectors. The sensitivity of graphene’s in-plane electronic conductivity to its immediate surface environment, as influenced by trans-electrode potential, will offer new insights into atomic surface processes and sensor development opportunities. (4-6).

A nanopore-based diagnostic tool could offer various advantages:

  • it could detect target molecules at very low concentrations from very small sample volumes;
  • it could simultaneously screen panels of biomarkers or genes (which is important in disease diagnosis,
  • monitoring progression and prognosis);
  • it could provide rapid analysis at relatively low cost; and
  • it could eliminate cumbersome amplification and conversion steps such as PCR, bisulphite conversion and Sanger sequencing

Nanopores are likely to have an increasing role in medical diagnostics and DNA sequencing in years to come, but they will face competition from a number of other techniques. These include

  • single-molecule evanescent field detection of sequencing-by-synthesis in arrays of nanochambers (Pacific Biosciences),
  • sequencing by ligation on self-assembled DNA nanoarrays (Complete Genomics), and the
  • detection of H+ ions released during sequencing-by-synthesis on silicon field-effect transistors from multiple polymerase-template reactions (Ion Torrent).

However, the possibility of using nanopore-based sensors to perform long base reads on unlabelled ssDNA molecules in a rapid and costeffective manner could revolutionize genomics and personalized medicine.

Current trends suggest that many challenges in sequencing with biological nanopores

  • the high translocation velocity and the
  • lack of nucleotide specificity

have been resolved. Similarly, given the progress with solid-state nanopores, if the

  • translocation velocity could be reduced to a single nucleotide (which is ~3Å long) per millisecond, and if
  • nucleotides could be identified uniquely with an electronic signature (an area of intense research),

it would be possible to sequence a molecule containing one million bases in less than 20 minutes. Furthermore, if this technology could be scaled to an array of 100,000 individually addressed nanopores operating in parallel, it would be possible to sequence an entire human genome (some three billion base pairs) with 50-fold coverage in less than one hour.

Although, none of the nanopore-solid base sequencing technique have been used as a tool in a clinical trial, one UK-based biotechnology company has its way, nanopore sequencing may soon be available to the public. Earlier this year 2012 Oxford Nanopore Technologies (ONT) announced that it was on the verge of manufacturing a commercial nanopore sensor. [The company said that by year’s end it would release a $900 handheld model, which it claims can sequence a virus genome 48 000 bases long, and a larger, scalable model that could decode a human genome in as little as 15 minutes. In contrast, conventional systems cost upward of $500 000 and take weeks to sequence a human genome (7).]

REFERENCES

** http://www.nature.com/nrclinonc/focus/personalized-medicine/index.html

1. http://www.azonano.com/article.aspx?ArticleID=3078

2. G.E. Marchant. Small is Beautiful: What Can Nanotechnology Do for Personalized Medicine?. Current Pharmacogenomics and Personalized Medicine, 2009, 7, 231-237http://www.benthamscience.com/cppm/Sample/cppm7-4/002AF.pdf

3. http://www.foresight.org/nanodot/?p=4992

4. Venkatesan BM and Bashi R. Nanopore sensors for nucleic acid analysis. Nature Nanotechnology 2011; 18: http://libna.mntl.illinois.edu/pdf/publications/127_venkatesan.pdf

5. Garaj S., Hubbard W., Reina A., King J., Branton D and Golovchenko JA. Graphene as a sub-nanometer trans-electrode membrane. Nature 2010 (9) 467(7312): 190-193. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956266/

6. Min SK., Kim WY., Cho Y and Kim KS. Fast DNA sequencing with a graphene-based nanochannel device. Nature Nanotechnology 2011; 6: 162-165.  http://biophy.nju.edu.cn/lablog/wp-content/uploads/2011/10/Fast-DNA-sequencing-with-a-graphene-based.pdf

7. http://www.physicstoday.org/resource/1/phtoad/v65/i11/p29_s1?bypassSSO=1

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