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Archive for the ‘Diagnostics and Lab Tests’ Category


Real Time @BIOConvention #BIO2019:#Bitcoin Your Data! From Trusted Pharma Silos to Trustless Community-Owned Blockchain-Based Precision Medicine Data Trials

Reporter: Stephen J Williams, PhD @StephenJWillia2
Speakers

As care for lifestyle-driven chronic diseases expands in scope, prevention and recovery are becoming the new areas of focus. Building a precision medicine foundation that will promote ownership of individuals’ health data and allow for sharing and trading of this data could prove a great blockchain.

At its core, blockchain may offer the potential of a shared platform that decentralizes healthcare interactions ensuring access control, authenticity and integrity, while presenting the industry with radical possibilities for value-based care and reimbursement models. Panelists will explore these new discoveries as well as look to answer lingering questions, such as: are we off to a “trustless” information model underpinned by Bitcoin cryptocurrency, where no central authority validates the transactions in the ledger, and anyone whose computers can do the required math can join to mine and add blocks to your data? Would smart contracts begin to incentivize “rational” behaviors where consumers respond in a manner that makes their data interesting?

Moderator:  Cybersecurity is extremely important in the minds of healthcare CEOs.  CEO of Kaiser Permenente has listed this as one of main concerns for his company.

Sanjeey of Singularity: There are Very few companies in this space.  Singularity have collected thousands of patient data.  They wanted to do predictive health care, where a patient will know beforehand what health problems and issues to expect.  Created a program called Virtual Assistant. As data is dynamic, the goal was to provide Virtual Assistant to everyone.

Benefits of blockchain: secure, simple to update, decentralized data; patient can control their own data, who sees it and monetize it.

Nebular Genetics: Company was founded by Dr. George Church, who had pioneered the next generation sequencing (NGS) methodology.  The company goal is to make genomics available to all but this currently is not the case as NGS is not being used as frequently.

The problem is a data problem:

  • data not organized
  • data too parsed
  • data not accessible

Blockchain may be able to alleviate the accessibiltiy problem.  Pharma is very interested in the data but expensive to collect.  In addition many companies just do large scale but low depth sequencing.  For example 23andme (which had recently made a big deal with Lilly for data) only sequences about 1% of genome.

There are two types of genome sequencing companies

  1.  large scale and low depth – like 23andme
  2. smaller scale but higher depth – like DECODE and some of the EU EXOME sequencing efforts like the 1000 Project

Simply Vital Health: Harnesses blockchain to combat ineffeciencies in hospital records. They tackle the costs after acute care so increase the value based care.  Most of healthcare is concentrated on the top earners and little is concentrated on the majority less affluent and poor.  On addressing HIPAA compliance issues: they decided to work with HIPAA and comply but will wait for this industry to catch up so the industry as a whole can lobby to affect policy change required for blockchain technology to work efficiently in this arena.  They will only work with known vendors: VERY Important to know where the data is kept and who are controlling the servers you are using.  With other blockchain like Etherium or Bitcoin, the servers are anonymous.

Encrypgen: generates new blockchain for genomic data and NGS companies.

 

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Lab on a chip Enters a New Field

Reporter: Irina Robu, PhD

The basis of the lab-on-a-chip is to integrate thousands of biochemical operations onto a single chip that could be done by splitting a single drop of blood collected from the patient in order to get a precise diagnosis of potential diseases. Research on lab-on-a-chip primarily focuses on human diagnostics and DNA analysis. Miniaturization of biochemical operations normally handled in a laboratory has numerous advantages, such as cost efficiency, diagnostic speed and sensitivity. The emergence of the lab-on-a-chip field mainly relies on two core technologies: microfluidics and molecular biology.

The team led by Govind Kaigala at IBM Research-Zurich and the group of Moran Bercovici at Technion-Israel Institute of Technology designed a new device that can effectively control liquids and materials on the micro-scale and have demonstrated that the key to dynamic control of fluid mechanics may be electric. Their research is published on Proceedings of the National Academy of Sciences.

The research team turned to electric field to control the control the motion of fluid in a way that is adjustable. When liquid contacts a surface, it develops a layer of charge; applying an electric field to this layer moves the charges, dragging the liquid with them and creating a net flow.

Using this knowledge, the team calculated a device that uses disk-shaped electrodes implanted in the bottom of a fluidic chamber to produce dipole-like flow patterns in the liquid when an electric field is applied. Placing multiple electrodes together in an array generates “virtual channels” that guide the fluid stream. By altering the voltages on the electrodes, they could then reverse the pattern to create an inner region of flow bounded by an outer region of stagnation, which is useful for selective on-demand mixing. While more applications of these flow patterns have yet to be explored, the control and flexibility the team’s device offers recommend that the lab-on-a-chip dream may finally be within grasp.

SOURCE

https://physicsworld.com/a/microfluidics-enters-a-new-field/

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

 

Gender of a person can affect the kinds of cancer-causing mutations they develop, according to a genomic analysis spanning nearly 2,000 tumours and 28 types of cancer. The results show striking differences in the cancer-causing mutations found in people who are biologically male versus those who are biologically female — not only in the number of mutations lurking in their tumours, but also in the kinds of mutations found there.

 

Liver tumours from women were more likely to carry mutations caused by a faulty system of DNA mending called mismatch repair, for instance. And men with any type of cancer were more likely to exhibit DNA changes thought to be linked to a process that the body uses to repair DNA with two broken strands. These biases could point researchers to key biological differences in how tumours develop and evolve across sexes.

 

The data add to a growing realization that sex is important in cancer, and not only because of lifestyle differences. Lung and liver cancer, for example, are more common in men than in women — even after researchers control for disparities in smoking or alcohol consumption. The source of that bias, however, has remained unclear.

In 2014, the US National Institutes of Health began encouraging researchers to consider sex differences in preclinical research by, for example, including female animals and cell lines from women in their studies. And some studies have since found sex-linked biases in the frequency of mutations in protein-coding genes in certain cancer types, including some brain cancers and advanced melanoma.

 

But the present study is the most comprehensive study of sex differences in tumour genomes so far. It looks at mutations not only in genes that code for proteins, but also in the vast expanses of DNA that have other functions, such as controlling when genes are turned on or off. The study also compares male and female genomes across many different cancers, which can allow researchers to pick up on additional patterns of DNA mutations, in part by increasing the sample sizes.

 

Researchers analysed full genome sequences gathered by the International Cancer Genome Consortium. They looked at differences in the frequency of 174 mutations known to drive cancer, and found that some of these mutations occurred more frequently in men than in women, and vice versa. When they looked more broadly at the loss or duplication of DNA segments in the genome, they found 4,285 sex-biased genes spread across 15 chromosomes.

 

There were also differences found when some mutations seemed to arise during tumour development, suggesting that some cancers follow different evolutionary paths in men and women. Researchers also looked at particular patterns of DNA changes. Such patterns can, in some cases, reflect the source of the mutation. Tobacco smoke, for example, leaves behind a particular signature in the DNA.

 

Taken together, the results highlight the importance of accounting for sex, not only in clinical trials but also in preclinical studies. This could eventually allow researchers to pin down the sources of many of the differences found in this study. Liver cancer is roughly three times as common in men as in women in some populations, and its incidence is increasing in some countries. A better understanding of its aetiology may turn out to be really important for prevention strategies and treatments.

 

References:

 

https://www.nature.com/articles/d41586-019-00562-7?utm_source=Nature+Briefing

 

https://www.nature.com/news/policy-nih-to-balance-sex-in-cell-and-animal-studies-1.15195

 

https://www.ncbi.nlm.nih.gov/pubmed/26296643

 

https://www.biorxiv.org/content/10.1101/507939v1

 

https://www.ncbi.nlm.nih.gov/pubmed/25985759

 

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Immunoediting can be a constant defense in the cancer landscape


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

 

There are many considerations in the cancer immunoediting landscape of defense and regulation in the cancer hallmark biology. The cancer hallmark biology in concert with key controls of the HLA compatibility affinity mechanisms are pivotal in architecting a unique patient-centric therapeutic application. Selection of random immune products including neoantigens, antigens, antibodies and other vital immune elements creates a high level of uncertainty and risk of undesirable immune reactions. Immunoediting is a constant process. The human innate and adaptive forces can either trigger favorable or unfavorable immunoediting features. Cancer is a multi-disease entity. There are multi-factorial initiators in a certain disease process. Namely, environmental exposures, viral and / or microbiome exposure disequilibrium, direct harm to DNA, poor immune adaptability, inherent risk and an individual’s own vibration rhythm in life.

 

When a human single cell is crippled (Deranged DNA) with mixed up molecular behavior that is the initiator of the problem. A once normal cell now transitioned into full threatening molecular time bomb. In the modeling and creation of a tumor it all begins with the singular molecular crisis and crippling of a normal human cell. At this point it is either chop suey (mixed bit responses) or a productive defensive and regulation response and posture of the immune system. Mixed bits of normal DNA, cancer-laden DNA, circulating tumor DNA, circulating normal cells, circulating tumor cells, circulating immune defense cells, circulating immune inflammatory cells forming a moiety of normal and a moiety of mess. The challenge is to scavenge the mess and amplify the normal.

 

Immunoediting is a primary push-button feature that is definitely required to be hit when it comes to initiating immune defenses against cancer and an adaptation in favor of regression. As mentioned before that the tumor microenvironment is a “mixed bit” moiety, which includes elements of the immune system that can defend against circulating cancer cells and tumor growth. Personalized (Precision-Based) cancer vaccines must become the primary form of treatment in this case. Current treatment regimens in conventional therapy destroy immune defenses and regulation and create more serious complications observed in tumor progression, metastasis and survival. Commonly resistance to chemotherapeutic agents is observed. These personalized treatments will be developed in concert with cancer hallmark analytics and immunocentrics affinity and selection mapping. This mapping will demonstrate molecular pathway interface and HLA compatibility and adaptation with patientcentricity.

References:

 

https://www.linkedin.com/pulse/immunoediting-cancer-landscape-john-catanzaro/

 

https://www.cell.com/cell/fulltext/S0092-8674(16)31609-9

 

https://www.researchgate.net/publication/309432057_Circulating_tumor_cell_clusters_What_we_know_and_what_we_expect_Review

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190561/

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5840207/

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5593672/

 

https://www.frontiersin.org/articles/10.3389/fimmu.2018.00414/full

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5593672/

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190561/

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388310/

 

https://www.linkedin.com/pulse/cancer-hallmark-analytics-omics-data-pathway-studio-review-catanzaro/

 

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Live Conference Coverage @Medcitynews Converge 2018 Philadelphia:Liquid Biopsy and Gene Testing vs Reimbursement Hurdles

9:25- 10:15 Liquid Biopsy and Gene Testing vs. Reimbursement Hurdles

Genetic testing, whether broad-scale or single gene-testing, is being ordered by an increasing number of oncologists, but in many cases, patients are left to pay for these expensive tests themselves. How can this dynamic be shifted? What can be learned from the success stories?

Moderator: Shoshannah Roth, Assistant Director of Health Technology Assessment and Information Services , ECRI Institute @Ecri_Institute
Speakers:
Rob Dumanois, Manager – reimbursement strategy, Thermo Fisher Scientific
Eugean Jiwanmall, Senior Research Analyst for Medical Policy & Technology Evaluation , Independence Blue Cross @IBX
Michael Nall, President and Chief Executive Officer, Biocept

 

Michael: Wide range of liquid biopsy services out there.  There are screening companies however they are young and need lots of data to develop pan diagnostic test.  Most of liquid biopsy is more for predictive analysis… especially therapeutic monitoring.  Sometimes solid biopsies are impossible , limited, or not always reliable due to metastasis or tough to biopsy tissues like lung.

Eugean:  Circulating tumor cells and ctDNA is the only FDA approved liquid biopsies.  However you choose then to evaluate the liquid biopsy, PCR NGS, FISH etc, helps determines what the reimbursement options are available.

Rob:  Adoption of reimbursement for liquid biopsy is moving faster in Europe than the US.  It is possible in US that there may be changes to the payment in one to two years though.

Michael:  China is adopting liquid biopsy rapidly.  Patients are demanding this in China.

Reimbursement

Eugean:  For IBX to make better decisions we need more clinical trials to correlate with treatment outcome.  Most of the major cancer networks, like NCCN, ASCO, CAP, just have recommendations and not approved guidelines at this point.  From his perspective with lung cancer NCCN just makes a suggestion with EGFR mutations however only the companion diagnostic is approved by FDA.

Michael:  Fine needle biopsies are usually needed by the pathologist anyway before they go to liquid biopsy as need to know the underlying mutations in the original tumor, it just is how it is done in most cancer centers.

Eugean:  Whatever the established way of doing things, you have to outperform the clinical results of the old method for adoption of a newer method.

Reimbursement issues have driven a need for more research into clinical validity and utility of predictive and therapeutic markers with regard to liquid biopsies.  However although many academic centers try to partner with Biocept Biocept has a limit of funds and must concentrate only on a few trials.  The different payers use different evidence based methods to evaluate liquid biopsy markers.  ECRI also has a database for LB markers using an evidence based criteria.  IBX does sees consistency among payers as far as decision and policy.

NGS in liquid biopsy

Rob: There is a path to coverage, especially through the FDA.  If you have a FDA cleared NGS test, it will be covered.  These are long and difficult paths to reimbursement for NGS but it is feasible. Medicare line of IBX covers this testing, however on the commercial side they can’t cover this.  @IBX: for colon only kras or nras has clinical utility and only a handful of other cancer related genes for other cancers.  For a companion diagnostic built into that Dx do the other markers in the panel cost too much?

Please follow on Twitter using the following #hash tags and @pharma_BI

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5:00 – 5:45 PM Early Diagnosis Through Predictive Biomarkers, NonInvasive Testing

Reporter: Stephen J. Williams, Ph.D.

 

Diagnosing cancer early is often the difference between survival and death. Hear from experts regarding the new and emerging technologies that form the next generation of cancer diagnostics.

Moderator: Heather Rose, Director of Licensing, Thomas Jefferson University
Speakers:
Bonnie Anderson, Chairman and CEO, Veracyte @BonnieAndDx
Kevin Hrusovsky, Founder and Chairman, Powering Precision Health @KevinHrusovsky

Bonnie Anderson and Veracyte produces genomic tests for thyroid and other cancer diagnosis.  Kevin Hrusovksy and Precision Health uses peer reviewed evidence based medicine to affect precision medicine decision.

Bonnie: aim to get a truth of diagnosis.  Getting tumor tissue is paramount as well as properly preserved tissue.  They use deep RNA sequencing  and machine learning  in their clinically approved tests.

Kevin: Serial biospace entrepreneur.  Two diseases, cancer and neurologic, have been diseases which have been hardest to get reproducible and validated biomarkers of early disease.  He concentrates on protein biomarkers.

Heather:  FDA has recently approved drugs for early disease intervention.  However the use of biomarkers can go beyond patient stratification in clinical trials.

Kevin: 15 approved drugs for MS but the markers are scans looking for brain atrophy which is too late of an endpoint.  So we need biomarkers of early disease progression.  We can use those early biomarkers of disease progression so pharma can target those early biomarkers and or use those early biomarkers of disease progression  for endpoint

Bonnie: exciting time in the early diagnostics field. She prefers transcriptomics to DNA based methods such as WES or WGS (whole exome or whole genome sequencing).  It was critical to show data on the cost savings imparted by their transcriptomic based thryoid cancer diagnostic test for payers to consider this test eligible for reimbursement.

Kevin: There has been 20 million  CAT scans for  cancer but it is estimated 90% of these scans led to misdiagnosis. Biomarker  development  has revolutionized diagnostics in this disease area.  They have developed a breakthrough panel of ten protein biomarkers in serum which he estimates may replace 5 million mammograms.

All panelists agreed on the importance of regulatory compliance and the focus of new research should be on early detection.  In addition they believe that Dr. Gotlieb’s appointment to the FDA is a positive for the biomarker development field, as Dr. Gotlieb understands the potential and importance of early detection and prevention of disease.  Kevin also felt Dr. Gotlieb understands the importance of incorporating biomarkers as endpoints in clinical trials.  Over 750 phase 1,2, and 3 clinical trials use biomarker endpoints but the pharma companies still need to prove the biomarkers clinical relevance to the FDA.They also agreed it would be helpful to involve advocacy groups in putting more pressure on the healthcare providers and policy makers on this importance of diagnostics as a preventative measure.

In addition, the discovery and use of biomarkers as disease endpoints has led to a resurgence of Alzheimer’s disease drug development by companies which have previously given up on these type of neurodegenerative diseases.

Kevin feels proteomics offers great advantages over DNA-based diagnostics, especially in cancer such as ovarian cancer, where a high degree of specificity for a diagnostic test is required to ascertain if a woman should undergo prophylactic oophorectomy.  He suggests that a new blood-based protein biomarker panel is being developed for early detection of some forms of ovarian cancer.

Please follow on Twitter using the following #hash tags and @pharma_BI

#MCConverge

#cancertreatment

#healthIT

#innovation

#precisionmedicine

#healthcaremodels

#personalizedmedicine

#healthcaredata

And at the following handles:

@pharma_BI

@medcitynews

 

Please see related articles on Live Coverage of Previous Meetings on this Open Access Journal

LIVE – Real Time – 16th Annual Cancer Research Symposium, Koch Institute, Friday, June 16, 9AM – 5PM, Kresge Auditorium, MIT

Real Time Coverage and eProceedings of Presentations on 11/16 – 11/17, 2016, The 12th Annual Personalized Medicine Conference, HARVARD MEDICAL SCHOOL, Joseph B. Martin Conference Center, 77 Avenue Louis Pasteur, Boston

Tweets Impression Analytics, Re-Tweets, Tweets and Likes by @AVIVA1950 and @pharma_BI for 2018 BioIT, Boston, 5/15 – 5/17, 2018

BIO 2018! June 4-7, 2018 at Boston Convention & Exhibition Center

https://pharmaceuticalintelligence.com/press-coverage/

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Centers for Medicare & Medicaid Services announced that the federal healthcare program will cover the costs of cancer gene tests that have been approved by the Food and Drug Administration

 

Reporter: Aviva Lev-Ari, PhD, RN

genetic testing just became routine care for patients with advanced cancers. And that means precision medicine has finally broken into the mainstream.

Any tests that gain FDA clearance in the future will automatically receive full coverage.

In 3/2018 there are three FDA approved Genetic Tests for Cancer:

UNDER development and not included in the agreement , above, includes:

  • Olivier Elemento, Director of the Caryl and Israel Englander Institute for Precision Medicine at Cornell, the team at Cornell, for example, has developed a whole exome test that compares mutations in tumors against healthy cells across 22,000 genes. To date, it’s been used to help match more than 1,000 patients in New York state with the best available treatment options.

Under the final decision, doctors are still free to order non-FDA approved tests, but coverage isn’t guaranteed; each case will be evaluated by local Medicare administrative contractors. Which means Elemento’s test could still be covered. “To me this is a vote of confidence that next generation sequencing is useful for cancer patients,” says Elemento.

So far, CMS is only covering these tests for stage three and stage four metastatic cancer sufferers. Most of them aren’t going to be cured. They might get a few more good months, maybe a year, tops.

Cancerous Genes

SOURCE

WITH MEDICARE SUPPORT, GENETIC CANCER TESTING GOES MAINSTREAM

https://www.wired.com/story/with-medicare-support-genetic-cancer-testing-goes-mainstream/?mbid=social_twitter_onsiteshare

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