Category Archives: Pharmacogenomics

By Turna Ray

Abbott Molecular plans to contact the British Journal of Cancer to contest the conclusions of a recently published cost-effectiveness analysis involving its Vysis ALK Break Apart FISH Probe Kit.

According to Stafford O'Kelly, president of Abbott Molecular, the authors of the study published in BJC last month based their economic analysis on two erroneous assumptions: the list price charged by labs for the ALK test and the prevalence of ALK rearrangements in the advanced non-small cell lung cancer population. As such, the modeling performed by the researchers to determine the circumstances under which the pharmacogenetic test is cost effective is flawed and should not be considered by healthcare providers and payors, Abbott maintained.

"If clinicians were to act on this article, patients will suffer," O'Kelly told PGx Reporter. "The whole premise of the paper is based fundamentally on very incorrect assumptions."

In the BJC paper, University of Colorado researchers Adam Atherly and Ross Camidge modeled the health economics of administering Pfizer's non-small cell lung cancer drug Xalkori to patients whose tumors are ALK mutation-positive. They found that broadly testing all advanced NSCLC patients in order to identify the small subset of ALK-positive individuals who should be treated with Xalkori did not meet a cost-effectiveness bar of less than $100,000 per quality-adjusted life year gained.

The US Food and Drug Administration last August simultaneously approved Pfizer's Xalkori and Abbott's Vysis ALK Break Apart FISH Probe Kit. The drug costs more than $115,000 per year. The $1,400 price tag for FISH-based ALK testing cited in the BJC analysis was established by "expert opinion" gathered by the researchers.

"Prices for the different tests vary depending on the payer and system. In the US, for example, different insurers reimburse charges at different rates. To limit this complexity, we have therefore taken charges, not reimbursements, as our base values," the study authors detail in the BJC article. "We estimated costs for pathological testing, including both technical and professional fees, utilizing Medicare list prices and the associated University of Colorado charges."

Assuming testing costs within a range of $600 to $1,400 per patient, Atherly and Camidge found that PGx testing for Xalkori is not cost-effective because ALK rearrangements occur in less than 5 percent of advanced NSCLC patients. However, the researchers demonstrated that by applying enrichment strategies to narrow the NSCLC population receiving testing for example, if physicians only tested those NSCLC patients who have adenocarcinoma histology, are non-smokers, and are known to have EGFR and KRAS wild-type tumors payors could potentially more than double the "mean health gain" to around 0.29 QALYs gained per person from 0.013 QALYs gained per person if all advanced NSCLC patients were genetically tested (PGx Reporter 3/21/2012).

In O'Kelly's view, the researchers should not have based their economic modeling on the list price labs charge for the test, but should instead have pegged the analysis to payor reimbursement rates. As the manufacturer, Abbott said it charges labs less than $170 per patient for the ALK FISH test kit. The laboratory then factors in costs associated with performing the test when billing for it.

The lab costs of between $600 and $1,400 cited in the study are "highly exaggerated," O'Kelly asserted. Furthermore, the list price doesn't accurately reflect what payors are reimbursing for the test, which in his view is the most important number when it comes to calculating what a medical intervention costs the healthcare system.

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Abbott Challenges 'Incorrect Assumptions' in Cost-Effectiveness Study of Xalkori PGx Testing

By Turna Ray

A study involving Agendia's MammaPrint test has shown that physicians may be able to use the test results alongside other clinical data to withhold chemotherapy for patients with a low risk of recurrence without impacting their five-year survival.

According to Agendia, the study marks the first prospectively designed outcomes trial to gauge whether the use of a molecular diagnostic can impact breast cancer survival by avoiding unnecessary and toxic treatment. Past data on MammaPrint and other breast cancer recurrence diagnostics have shown that such tests impact treatment decisions and can impact survival, but in those investigations, researchers performed genomic analysis retrospectively on samples from patients previously enrolled in large studies.

Data from the Microarray Prognostics in Breast Cancer, or RASTER, study showed that the use of MammaPrint led to a 20 percent reduction in adjuvant chermotherapy use in patients whom the test determined to be at low risk of recurrence.

"Based on our data, the use of the genomic test could lead to a reduction of nearly 30 percent in the use of adjuvant chemotherapy without compromising patient outcomes," lead study investigator Sabine Linn of the Netherlands Cancer Institute said in a statement. In clinical practice, "this percentage may vary somewhat due to different guidelines used in different countries."

In RASTER, between 2004 and 2006, researchers collected fresh tumor samples from 427 women who were younger than 61 years and had breast cancer that hadn't yet spread to the lymph nodes. The researchers then analyzed these samples with MammaPrint, a microarray-based test that measures the expression of 70 genes.

Those patients deemed by MammaPrint to be at high risk of cancer recurrence were provided adjuvant chemotherapy. In the case of patients deemed to be at low risk, physicians considered both the MammaPrint results and clinical factors to decide whether they could avoid receiving such treatment. After patients were treated, study investigators followed them for five years to gauge outcomes.

Within the 219 patients in the low-risk group, 85 percent avoided chemotherapy while the remainder received it because their clinical factors suggested they might benefit from it, Bastiaan van der Baan, VP of sales and marketing at Agendia, told PGx Reporter.

In the high-risk group, meanwhile, 81 percent of 208 patients received chemotherapy.

The low risk group experienced a five-year distant disease-free survival rate of 96 percent versus a DDFS rate of 90 percent in the high-risk group.

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Prospective Outcomes Trial Shows Agendia's MammaPrint Safely Reduces Chemo Use in Low-Risk Patients

By Uduak Grace Thomas

SAN FRANCISCO, Calif. The Electronic Medical Records and Genomics Network has launched an open resource, dubbed the Phenotype KnowledgeBase, which offers access to validated algorithms for identifying patients with specific disease phenotypes based on data in their electronic medical records.

Joshua Denny, an assistant professor in the biomedical informatics and medical departments at eMERGE participant Vanderbilt University, described the new resource at the American Medical Informatics Association's Summit on Translational Bioinformatics here this week.

PheKB currently includes 12 algorithms developed by members of the eMERGE consortium, though others are welcome to contribute their tools, Denny told BioInform.

The algorithms use natural language processing techniques to mine EMR data for patients with particular conditions of interest to researchers, such as cataracts, Alzheimers disease, low levels of high-density lipoprotein, type II diabetes, among others.

These algorithms make their selections using various search criteria, such as ICD9 codes, current procedural terminology codes, laboratories, and medications, according to the website.

Scientists from the consortium have been using the algorithms for a number of projects, including a study published last April in which they mined data from five institutions to find patients in each of five disease groups (BI 04/22/0011).

Denny explained that the consortium developed the database so that its tools could be better disseminated to other research efforts that are also studying disease phenotypes such as the Pharmacogenomics Research Network.

Initially, the eMERGE algorithms were made available through the consortiums Wikipedia page, but that method did not allow the kind of interactivity the researchers were looking for, Denny said.

Through PheKB, users can share their own tools as well as any updates that they make to existing algorithms on the website, he said.

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EMERGE Network Launches Publicly Available Database of Phenotype Identification Algorithms

By Turna Ray

Quest Diagnostics has launched a renal transplant rejection test that the company claims can help doctors figure out if their patients are rejecting their new kidneys "weeks before" clinical symptoms or other standard tests can detect such events.

Kidney transplant rejection is a costly and common occurrence. Quest believes that its blood-based, non-invasive Renal Transplant Monitoring test, if widely adopted, can save the healthcare system money by obviating the need for the more expensive tests currently in use.

Quest developed the laboratory test in collaboration with Beth Israel Deaconess Medical Center and Weill Cornell Medical College. The company claims that it is the first commercial molecular diagnostic for kidney transplant rejection.

The real-time PCR-based test gauges several RNA markers, including FoxP3, GZMB, and PRF1, which Quest exclusively licensed from Beth Israel and Weill.

Terry Strom, co-director of The Transplant Institute at Beth Israel, along with Manikkam Suthanthiran, chairman of the Department of Transplantation Medicine at Weill, have published data showing that biomarkers such as FoxP3 and others are useful in detecting acute cellular rejection of renal transplants.

Researchers from Weill Cornell and elsewhere have published studies in several peer-reviewed journals demonstrating an association between the RNA markers in Quest's panel and renal transplant rejection. Rises in blood RNA levels "often occur before a rise in blood levels of serum creatinine," Quest said in a statement. As such, the Renal Transplant Monitoring test may allow doctors to predict earlier that their patients are at risk of transplant rejection and take action to prevent this from happening.

Wendy Bost, director of media relations at Quest, told PGx Reporter that the company "validated the test in the performing laboratory prior to release."

In 2009, there were nearly 17,000 renal transplant procedures performed, making the kidney the most routinely transplanted organ. However, based on 2010 figures from the US Organ Procurement and Transplantation Network and the Scientific Registry of Transplant Recipients, 70 percent of kidney transplants from a deceased donor fail within five years.

Current standard procedures for assessing whether a patient is rejecting a kidney transplant involve checking serum creatinine levels to gauge renal function and performing biopsies of the kidney, which can result in bleeding, graft injury, or loss.

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Quest Launches MDx that May Predict Kidney Transplant Rejection Earlier than Current Methods

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/132bc6/bioinformatics_mar) has announced the addition of the "Bioinformatics Market Outlook to 2015" report to their offering.

During the past decade, the bioinformatics market has significantly evolved across the globe on back of rising genomics industry. The increasing application of genomics in biotech and pharmaceutical research and development has created a huge commercial market for bioinformatics worldwide. As per our latest research report's estimation, the global bioinformatics market, which reached the mark of around US$ 3 Billion in 2010, will expand at a CAGR of around 25% during 2012-2015 as the declining cost of human genome sequencing and increasing public and private sector investment will give a significant boost to the industry.

According to Bioinformatics Market Outlook to 2015, the content market that includes specialized and generalized databases was the biggest segment of the global bioinformatics industry in 2010, followed by analysis software & services and IT infrastructure. As per our analysis, the software segment is likely to exhibit strong performance in future, improving its share in the overall market. On the other hand, content/database market will suffer the downturn due to the increasing popularity of innovative analysis software. We have also discussed in the report how the free databases would impact the sales of the paid ones. Our report analyzed the wide application of bioinformatics in genomics, proteomics and pharmacogenomics. A further in-depth study of the market revealed that genome studies have completely transformed cancer research in the past few years and oncology has become the leading therapeutic area supported by bioinformatics. We also observed that small firms in the field are opting for outsourcing route to expand their presence. The other key trends and drivers pushing the market have also been elaborated in the comprehensive research study.

Read more inside Bioinformatics Market Outlook to 2015

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For more information visit http://www.researchandmarkets.com/research/132bc6/bioinformatics_mar

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Research and Markets: Bioinformatics Market Outlook to 2015

By Uduak Grace Thomas

Bioinformatics startup PanGenX is betting that its semantic approach to data integration will ultimately help drug developers and diagnostic firms develop more personalized treatments.

The firm, based in Auburndale, Mass., intends to help pharma and diagnostic customers integrate proprietary and public data in "meaningful ways" and then run analyses that reveal information on individuals' responses to treatment, Jeremy Sohn, PanGenX's chief operating officer, explained to BioInform this week

The company markets the PanGenX Knowledge Base, which uses a linked data approach to aggregate pharmacogenetic data, results from peer-reviewed literature, health outcomes, and claims data. It relies on a set of proprietary ontologies that specify scientific, clinical, and business concepts and relationships to structure that data for querying and analysis.

Among the data included in the knowledgebase is a version of the National Center for Biotechnology Information's Single Nucleotide Polymorphism Database, or dbSNP, that improves on the publicly available resource, according to PanGenX.

The company's version, dubbed LD-SNP, offers a cleaner, normalized version of the public resource, which makes it possible to find additional variants that aren't currently associated with some genes in dbSNP, Sohn explained.

For example, he said, dbSNP's record of the DPYD gene which encodes for the dihydropyrimidine dehydrogenase enzyme that is involved in a metabolic pathway reports about 6,000 variants for the gene, while PanGenX's approach identified nearly 12,000 variants.

This data, combined with the company's semantic-based approach to analysis, makes it possible to map and compare polymorphisms between different individuals as well as calculate distributions of variants from a gene, drug, or disease perspective, PanGenX said.

The product also includes so-called PURL (Persistent Uniform Resource Locator) Nexus, or Plexus, technology, which lets the system combine data from the knowledgebase with remote customer data.

Currently, PanGenX offers two versions of its knowledgebase under a software-as-a-service business model: PanGenx-KB, priced at $250,000 per year for a site license, is geared toward pharma and diagnostic companies; while PanGenX-KB Professional, priced at $35,000 per year, is meant for academic and commercial research groups and labs.

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PanGenX Takes Semantic-based Approach to Data Integration, Analytics for Personalized Medicine