EMERGE Network Launches Publicly Available Database of Phenotype Identification Algorithms

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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

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

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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

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

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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

Research and Markets: Bioinformatics Market Outlook to 2015

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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

Companies Mentioned:

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

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Research and Markets: Bioinformatics Market Outlook to 2015

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

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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

Pharmacogenomics – Video

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13-03-2012 12:01 Pentucket Medical cardiologists Sunny Biliazarian and Sunny Srivastava discuss the influence of our genetics impacts the our response to different medications. To speak with a Pentucket Medical cardiologist, please call: Haverhill, MA: (978) 521-3288 RiverWalk in Lawrence, MA: (978) 557-8900 Newburyport, MA: (978) 499-7400

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Pharmacogenomics - Video

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

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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

With MDx Usage and Costs on the Rise, UnitedHealthCare Urges Reimbursement Reform

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By Turna Ray

Amid rising adoption and costs of molecular diagnostics to personalize treatment decisions, insurer UnitedHealthCare is calling for improvements in the medical claims coding system that will enable accurate test utilization tracking.

In a working paper released this week by its Center for Health Reform & Modernization, UnitedHealthcare also advocates payor-supported clinical utility studies to demonstrate that molecular tests are improving patient outcomes and reducing healthcare costs.

"Reimbursement approaches used today, which involve setting an initial rate and subsequent indexing for inflation, may not reflect appropriately the value to the delivery system of a new technology and its continued use," UHC states in the report. "They also may contribute to the rising costs of new and complex tests. New approaches are needed and the working paper discusses some of the options."

In the paper, the insurer reports that its health plan participants racked up nearly $500 million in genetic and molecular diagnostic testing costs in 2010, a 14 percent increase on a per-person basis since 2008. Overall, national spending on genetic tests and molecular diagnostics "may have reached around $5 billion" in 2010 and could reach as high as $25 billion by 2021, according to the report.

The report also includes the results of a survey of consumers and physicians to gauge their attitudes about genetic testing. A poll of more than 1,200 physicians showed that more than 75 percent of doctors identified the cost of tests and reimbursement issues as the most difficult barrier to incorporating genetic tests in their practice.

Given that the US healthcare system is spending more on molecular diagnostics that will likely get more complex with advancing knowledge about the human genome, UHC makes a number of recommendations that could help payors ensure that they are paying for tests that are robustly validated, improve patient outcomes, and ultimately reduce healthcare costs.

"A new coding system could be a foundation for better analytics, evidence development and coverage," UHC states. "Such a system would assign specific codes to individual genetic tests and genetic testing services."

UHC's recommendations come amid a number of ongoing efforts to update the molecular diagnostic coding system.

The American Medical Association has created a two-tier current procedural terminology coding system for single analyte molecular diagnostics that will likely move into use next year. The AMA has also begun issuing Category 1 codes for multi-analyte, algorithm-based assays, such as Vermillion's OVA1 ovarian cancer test (PGx Reporter 3/7/2012).

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With MDx Usage and Costs on the Rise, UnitedHealthCare Urges Reimbursement Reform

Bioinformatics Market Outlook to 2015

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NEW YORK, March 15, 2012 /PRNewswire/ --Reportlinker.com announces that a new market research report is available in its catalogue:

http://www.reportlinker.com/p0795432/Bioinformatics-Market-Outlook-to-2015.html#utm_source=prnewswire&utm_medium=pr&utm_campaign=Genomics

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.

The market has witnessed the launches of key bioinformatics products and services in various areas, and we have evaluated these on the basis of their companies and countries in our report. The research includes country-level analysis and looks into the recent developments that may impact the industry's future performance in a significant manner. By providing a brief profile of key market players like Accelrys and Affymetrix and evaluating their recent activities in the study, we have presented the industry's competitive landscape. Overall, the report aims at providing an in-depth knowledge about the global bioinformatics market to clients and investors.1. Analyst View2. Research Methodology3. Key Industry Trends and Drivers3.1 Increasing Bioinformatics R&D Efforts by Players3.2 Strategic Collaborations Aimed at Enhancing Innovations3.3 Financial Support by Governments Strengthening Bioinformatics Research3.4 Oncology Research - Leading Therapeutic Area Being Aided by Bioinformatics3.5 Small Firms Enlarging Presence through Bioinformatics Outsourcing3.6 IT and Internet Growth Boosting Usage of Bioinformatics Tools4. Market Overview4.1 By Segment4.1.1 Analysis Software & Services4.1.2 Content/Database4.1.3 IT Infrastructure4.2 By Application4.2.1 Genomics4.2.2 Proteomics4.2.3 Pharmacogenomics5. Prominent Country Profile5.1 US5.2 UK5.3 Japan5.4 India5.5 China5.6 South Korea5.7 Taiwan5.8 Singapore5.9 Australia6. Recently Commercialized Products and Services7. Key Players7.1 Accelrys, Inc.7.2 Affymetrix, Inc.7.3 Compugen Ltd.7.4 IBM Life Sciences7.5 Kinexus

List of Figures:

Figure 4-1: Global - Cost of Genome Sequencing (US$), 1990 to 2015Figure 4-2: Global - Bioinformatics Market (Billion US$), 2010-2015Figure 4-3: Global - Bioinformatics Market by Segment (%), 2010Figure 4-4: Global - Analysis Software & Services Market (Million US$), 2010-2015Figure 4-5: Global - Content Market (Million US$), 2010-2015Figure 4-6: Global - IT Infrastructure Market (Million US$), 2010-2015Figure 4-7: Global - Bioinformatics IT Infrastructure Market by Segment (%), 2010Figure 4-8: Global - DNA Sequencing Market (Billion US$), 2010-2015Figure 4-9: Global - Proteomics Market (Billion US$), 2010-2015Figure 4-10: Global - Pharmacogenomics Market by Segment (%), 2009Figure 5-1: UK - Bioinformatics Market (Million US$), 2010-2015Figure 5-2: India - Bioinformatics Market (Billion INR), 2010-2015Figure 5-3: South Korea - Bioinformatics Market (Million US$), 2010-2015

List of Tables:

Table 4-1: Key Molecular Dynamics SoftwareTable 4-2: Key Molecular Modeling SoftwareTable 4-3: Key Open Source Bioinformatics SoftwareTable 4-4: Types of Generalized DatabasesTable 4-5: Types of Specialized DatabasesTable 4-6: Top Countries for High Content Analysis ResearchTable 4-7: Growth in Key Bioinformatics Databases (Dec 2010 & Dec 2011)Table 4-8: Top Countries for DNA Sequence Analysis ResearchTable 4-9: Key Genome Interpretation Databases and ResourcesTable 4-10: Available Data Sources and Gene Prioritization ToolsTable 4-11: Single Nucleotide Variants Interpretation ToolsTable 4-12: Top Countries for Proteomics ResearchTable 4-13: Mass Spectrometry E-ProgramsTable 4-14: 2-DE E-DatabasesTable 4-15: Key Pharmacogenomic DatabasesTable 4-16: Top Ten PharmGKB Gene, Drug, Disease and Pathway Pages (2009)Table 5-1: Top Countries for Bioinformatics ResearchTable 6-1: Recently Commercialized Bioinformatics ProductsTable 6-2: Recently Commercialized Bioinformatics Services

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Bioinformatics Market Outlook to 2015

WSU recruits geneticists in new research venture

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Washington State University is recruiting two genetics researchers to its Spokane campus to launch a $15 million enterprise that will add 135 pharmaceutical scientists.

It's a bold research and job creation that relies, in part, on leveraging a $1.2 million investment of local tax dollars with federal, state and private funds.

"These are people and projects that can be a real catalyst for Spokane," said Susan Ashe, acting executive director of the Health Sciences & Services Authority of Spokane County.

Called the HSSA, the authority was established several years ago to capture a sliver of the local-option sales taxes collected in the Spokane area to help pay for projects designed to create a thriving research cluster here.

If successful, the projects will turn into either sustained research facilities that create jobs, or they will produce ideas or goods that can be commercialized.

Philip Lazarus, a professor and researcher at Penn State University's College of Medicine, has been offered a position to erect a new academic and research program at WSU, a rare opportunity that WSU is dangling as a recruitment tool along with a generous financial package.

The authority is contributing $500,000 over two years to help bring Lazarus to Spokane and set up his program.

"This is pretty exciting stuff. An opportunity in academic research to really create something with your stamp on it," said Gary Pollack, WSU vice provost for health sciences.

Lazarus would work as WSU's chairman of pharmaceutical sciences at the Spokane campus starting in 2014.

His area of expertise is molecular genetics. Specifically, Lazarus is interested in pharmacogenomics. He would bring his independent, federally funded research with him.

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WSU recruits geneticists in new research venture

WSU venturing into pharmacogenomics – Tue, 13 Mar 2012 PST

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March 13, 2012 in City Researchers wooed to organize $15 million researchcenter

The HSSA was established several years ago to capture some of the local-option sales taxes collected in the Spokane area to help pay for projects designed to create a thriving research cluster in thearea.

Washington State University is recruiting two genetics researchers to its Spokane campus to launch a $15 million research enterprise that will add 135 pharmaceuticalscientists.

Its a bold research and job-creation effort announced Monday that relies in part on leveraging a $1.2 million investment of local tax dollars with federal, state and privatefunds.

These are people and projects that can be a real catalyst for Spokane, said Susan Ashe, acting executive director of the Health Sciences & Services Authority of SpokaneCounty.

Called the HSSA, the authority was established several years ago to capture a sliver of the local-option sales taxes collected in the Spokane area to help pay for projects designed to create a thriving research clusterhere.

If successful, the projects will turn into either sustained research facilities that create jobs, or they will produce ideas or goods that can becommercialized.

Philip Lazarus, a professor and researcher at Penn State Universitys College of Medicine, has been offered a position to erect a new academic and research program at WSU, a rare opportunity that WSU is dangling as a recruitment tool along with a generous financial package. The HSSA is contributing $500,000 over two years to help bring Lazarus to Spokane and set up hisprogram.

This is pretty exciting stuff. An opportunity in academic research to really create something with your stamp on it, said Gary Pollack, WSU vice provost for healthsciences.

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WSU venturing into pharmacogenomics - Tue, 13 Mar 2012 PST

Research and Markets: Stephens' Detection and Evaluation of Adverse Drug Reactions: Principles and Practice (6th …

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DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/831b19/stephens_detectio) has announced the addition of John Wiley and Sons Ltd's new book "Stephens' Detection and Evaluation of Adverse Drug Reactions: Principles and Practice (6th Edition)" to their offering.

Written with practitioners in mind, this new edition of Stephen's Detection of Adverse Drug Reactions: Principle and Practice continues to be one of the corner stones of the pharmaceutical medicine list. The classic text covers the issues and problems involved in the detection of adverse drug reactions (ADRs) throughout the life cycle of a medicine from animal studies through to clinical trials, its introduction to the market, followed by wide clinical use, and eventual decline in use or withdrawal. The sixth edition is completely revised and updated including five new chapters on pharmacogenomics, ADRs with herbal medicines, safety of medical devices, safety issues with oncology drugs, and economic aspects of ADRs. All tables and web information needed in order to practice are included to make this sixth edition a complete primer for the new practitioner and a reference for the more experienced.

Key Topics Covered:

Authors:

John Talbot, Senior Lecturer, University of Hertfordshire, UK. Formerly Director, Global Drug Safety, AstraZeneca R&D Charnwood, Loughborough, Leicestershire, UK

Jeffrey Aronson, Reader in Clinical Pharmacology, University of Oxford, Oxford, UK and President Emeritus of the British Pharmacological Society

For more information visit http://www.researchandmarkets.com/research/831b19/stephens_detectio

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Research and Markets: Stephens' Detection and Evaluation of Adverse Drug Reactions: Principles and Practice (6th ...

AMA Approves Vermillion MAAA Category 1 Code for OVA1; Will it Improve Reimbursement?

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By Turna Ray

The American Medical Association's Current Procedural Terminology Editorial Panel has approved Vermillion's application for a Category 1 CPT code for its OVA1 test.

According to a published summary of the panel's February meeting, the AMA "accepted establishment of code 814XX1 to describe the OVA1 test." The OVA1 test will also be listed in a new appendix for multi-analyte assays with algorithmic analysis, a subset of tests also known as in vitro diagnostic multivariate index assays.

The AMA decided a few months back that it would grant Category 1 codes to MAAAs that its CPT panel has vetted and found to meet a certain set of criteria. In addition to being listed under Category 1 codes, these tests will also be listed in a special section for MAAAs, called Appendix X. MAAAs that the AMA has not reviewed or that have not met coding criteria under Category 1 will only be listed in Appendix X. Tests in this appendix will be referenced by their proprietary names (PGx Reporter 11/9/2011).

At the February meeting, AMA's CPT panel added a new Category I subheading and guidelines in the "pathology and laboratory" section for MAAAs; established codes (ie. 81499X) to describe unlisted MAAAs with algorithmic analyses; established three new MAAA codes for listing in Appendix X; and revised its chemistry guidelines to include instructions for reporting unlisted MAAA codes.

Other than OVA1, the other two MAAAs that will be listed in Appendix X include a qualitative serum test that uses an algorithm to combine the results of two analytes and women's menopausal status into a numeric score, and a "diabetes pre-diagnostic risk screen" that analyzes multiple analytes to give a single risk score correlated with the probability of developing the disease.

The new MAAA codes will be effective Jan. 1, 2013.

According to Vermillion, in order to garner approval from the AMA for a Category 1 code, the company submitted several peer-reviewed publications on OVA1. Furthermore, the company said the fact that the test has been accepted for coverage by other payers, including Medicare contractor Highmark Medicare Services, also helped. "The new CPT code is a critical step in advancing the commercialization of OVA1, as we believe it will help streamline claims processing and accelerate further coverage and adoption by private payers," Vermillion CEO Gail Page said in a statement.

Currently there are three types of CPT codes payors use to process claims: Category I, II, and III. Many sponsors of IVDMIAs are currently using unlisted or miscellaneous codes under Category I to garner reimbursement for performed tests.

For example, Genomic Health's Oncotype DX is reimbursed with a miscellaneous CPT code and Agendia's MammaPrint uses the CPT code 84999 for "an unlisted chemistry procedure." Some MAAA providers claim to have good reimbursement through this process, but most have acknowledged that reimbursement agreements for tests with miscellaneous or unlisted codes have to be secured payor by payor, which is a costly and time-consuming process.

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AMA Approves Vermillion MAAA Category 1 Code for OVA1; Will it Improve Reimbursement?

USPSTF Updating BRCA Testing Recommendations for Asymptomatic Women; Accepting Public Input

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By Turna Ray

The US Preventative Services Task Force is seeking public comments on its systematic evidence review plan to assess under what conditions genetically testing asymptomatic women for their risk of developing hereditary breast and ovarian cancer has a positive impact on their health.

The USPSTF is in the process of updating its recommendation on BRCA mutation testing to gauge breast and ovarian cancer susceptibility. As part of that larger effort, it is calling for stakeholder input as it gathers evidence to answer specific questions on the risks and benefits of genetically testing asymptomatic women, who have a family history of breast and ovarian cancer but who themselves don't have these diseases.

The USPSTF's most recent recommendations on BRCA testing, issued in 2005, advise doctors against giving their patients routine referrals for genetic counseling or BRCA testing unless their family history suggests they might harbor mutations in tumor suppressor genes BRCA1 and BRCA2. The group recommends that if women have a family history that places them at increased risk for having these gene mutations, then doctors should refer them for genetic counseling and "evaluation for BRCA testing."

According to the National Cancer Institute, among Caucasian women in the US, between 5 percent and 10 percent of breast cancer patients and between 10 percent and 15 percent of ovarian cancer patients have BRCA1 and BRCA2 mutations. The risk of having these mutations is higher in women of Ashkenazi Jewish descent and those of Norwegian, Dutch, and Icelandic ethnicities. There is, however, limited data on how frequent these mutations occur among prevalent ethnic groups in the US, including African Americans, Hispanics, and Asian Americans.

"Although there currently are no standardized referral criteria, women with an increased-risk family history should be considered for genetic counseling to further evaluate their potential risks," the USPSTF notes in its 2005 recommendations. "Computational tools are available to predict the risk for clinically important BRCA mutations (that is, BRCA mutations associated with the presence of breast cancer, ovarian cancer, or both), but these tools have not been verified in the general population."

According to the USPSTF's proposal for comment, the group is seeking to gather evidence on whether BRCA testing reduces the incidence of breast and ovarian cancer, as well keeps women alive longer. Additionally, the USPSTF is seeking to gather data on how accurate physicians' risk assessment methods are for selecting which patients should receive BRCA mutation testing; what the benefits are of genetic counseling patients ahead of testing; and what the adverse effects of testing and counseling are.

USPSTF recommendations are carefully considered by private payors and factored into their coverage determinations for BRCA genetic testing. For example, Aetna in its clinical policy for BRCA testing cites the 2005 USPSTF recommendations to note that clinical models currently employed in medical practice for determining when women should receive genetic testing are based on women who already have cancer, and that the applicability of these models to screen asymptomatic or cancer-free women for BRCA testing is unknown.

"Available evidence suggests that current models for predicting BRCA mutation may tend to overestimate risk when family history is adequate and underestimate risk when family history is limited," Aetna states in the clinical policy. "Researchers have speculated that, in young women with limited family structures (i.e., fewer than two women who survived past age 45 in either parental lineage), the genetic models that are used to predict carrier status would underestimate the prevalence of BRCA mutations."

If USPSTF broadens its recommendations to include the asymptomatic population, it would certainly have a positive impact on Myriad Genetics' revenues for the BRACAnalysis test, the only commercially available genetic test that assesses BRCA mutations for hereditary breast and ovarian cancer susceptibility.

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USPSTF Updating BRCA Testing Recommendations for Asymptomatic Women; Accepting Public Input

Global Biochips Market to Reach US$4.6 Billion by 2017, According to New Report by Global Industry Analysts, Inc.

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GIA announces the release of a comprehensive global report on Biochips markets. Global market for Biochips is projected to reach US$4.6 billion by the year 2017. A promising market on the growth curve, Biochips are opening up new avenues for research and science, owing to the trend towards miniaturisation, parallelisation and the high alacrity of analysis. Besides genome analysis, Biochips are increasingly finding use in areas such as protein, diagnostics, toxicological, and biochemical research applications.

San Jose, CA (PRWEB) March 09, 2012

As stated by the new market research report on Biochips, the US continues to remain the largest regional market, with its technological superiority. Segment-wise, DNA Chips constitute the largest market. Despite plummeting market share, the segment is likely to continue its dominance in the biochip products market through 2017. Global Protein Biochips market is set for robust growth driven by anticipated rise in demand from proteomics and gene expression profiling applications. Gene expression profiling is expected to continue as the leading application area for biochips, while pharmacogenomics is expected to register robust growth.

Major players in the marketplace include Affymetrix Inc., Agilent Technologies., Bio-Rad Laboratories Inc., Caliper Life Sciences Inc., Cepheid Inc., Fluidigm Corporation, GE Healthcare Ltd., Illumina, Inc., and Life Technologies Corporation, among others.

The research report titled "Biochips: A Global Strategic Business Report" announced by Global Industry Analysts, Inc., provides a comprehensive review of trends, issues, strategic industry activities, and profiles of major companies worldwide. The report provides market estimates and projections (US$ Million) for the years 2009 through 2017 across global and regional markets for product segments including DNA Chips, Protein Chips, and Lab Chips. Geographic markets analyzed include the US, Canada, Japan, Europe, and Rest of World.

For more details about this comprehensive market research report, please visit

http://www.strategyr.com/Biochips_Market_Report.asp

About Global Industry Analysts, Inc.

Global Industry Analysts, Inc., (GIA) is a leading publisher of off-the-shelf market research. Founded in 1987, the company currently employs over 800 people worldwide. Annually, GIA publishes more than 1300 full-scale research reports and analyzes 40,000+ market and technology trends while monitoring more than 126,000 Companies worldwide. Serving over 9500 clients in 27 countries, GIA is recognized today, as one of the world's largest and reputed market research firms.

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Global Biochips Market to Reach US$4.6 Billion by 2017, According to New Report by Global Industry Analysts, Inc.

Transgenomic Reports Fiscal Year 2011 Financial Results

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OMAHA, Neb.--(BUSINESS WIRE)--

Transgenomic, Inc. (OTCBB: TBIO.OB - News) today reported financial results for the year ended December 31, 2011 and provided a business update.

Transgenomic enjoyed a landmark year in 2011, with revenue growth quarter-over-quarter and year-over-year as well as an attention to expense management translating into positive modified EBITDA for both the fourth quarter and full year 2011 periods, said Craig Tuttle, President and Chief Executive Officer. Our year-over-year top line increase of 59%, to $32 million in revenue for 2011, reflects growth in both our clinical reference labs and pharmacogenomics lab businesses. These encouraging top- and bottom-line results were achieved without compromising our investment in the development of groundbreaking new technologies. Supporting our strategic direction, and adding substantially to shareholder equity, was a $22 million private placement financing executed last month with a number of top-tier life sciences investors.

Mr. Tuttle continued: 2012 promises to be yet another important year for growth and value creation, as we look to build momentum behind our recently launched products, including our proprietary clopidogrel response panel, expand on our growing position as a key partner in cancer research and develop the markets where our products and services are available. As always, we will continue to focus on the successful integration of new products and technologies and expansion into new markets, all while managing toward the bottom line.

Recent Corporate and Business Events

Fourth Quarter and Fiscal Year Financial Results

Total revenue for the fourth quarter 2011 was $8.6 million, an increase of 68 percent compared with $5.1 million for the same period of 2010. Revenues for the fourth quarter of 2011 included $4.6 million in sales related to the Clinical Labs business, $0.5 million in revenue related to the Pharmacogenomics Services Unit (Pharma which supports Clinical Trials) and $3.5 million in revenue related to the Diagnostic Tools unit.

For the year ended December 31, 2011, revenues were $32.0 million, an increase of 59 percent compared with $20.0 million for the same period of 2010. This included $16.0 million in net sales related to the Clinical Labs, $2.3 million in Pharma revenues and $13.7 million in revenues related to the Diagnostic Tools unit.

Gross profit was $5.3 million, or 62 percent of net sales during the fourth quarter of 2011, compared with gross profit of $2.4 million, or 47 percent of net sales during the comparable period of 2010. Gross profit was $18.4 million, or 58 percent of net sales for 2011, compared with gross profit of $9.8 million, or 49 percent of net sales for 2010. The improvement in gross margin for the fourth quarter and full year is attributable to improvement in our Lab Services and Pharmacogenomic margins. The improvement in our Lab Services is due to the revenue from the FAMILION acquisition and successful consolidation of operations and reduction of overhead costs. Our Pharmacogenomics margins have improved due to the revenue increase quarter-over-quarter and year-over-year as the costs in that segment are relatively fixed.

Operating expenses were $5.4 million during the fourth quarter of 2011, compared to $3.7 million during the same period of 2010. Operating expenses increased primarily due to the acquisition of the FAMILION business, including non-cash charges totaling $0.3 million related to the amortization of the acquired intangibles. Operating expenses for the year ended December 31, 2011 were $21.4 million, compared with $13.4 million for 2010. Operating expenses increased primarily due to the acquisition of the FAMILION business, including non-cash charges for amortization related to the acquired intangibles of $1.2 million. We also recorded non-cash charges for stock option expenses of $1.0 million and bad debt expense of $1.7 million.

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Transgenomic Reports Fiscal Year 2011 Financial Results

Transgenomic's Q4 Revenues Increase 69 Percent

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By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) Transgenomic today reported 69 percent revenue growth year over year for the fourth quarter.

For the period ended Dec. 31, 2011, the Omaha, Neb.-based firm posted $8.6 million in revenues, up from $5.1 million a year ago. The Clinical Labs business recorded $4.6 million in revenue, Diagnostic Tools saw $3.5 million in revenues, and Pharmacogenomics had $500,000 in revenues.

Its R&D costs increased 60 percent to $568,000 from $354,000 a year ago, and SG&A costs rose 48 percent to $4.9 million from $3.3 million.

A net loss of $767,000, or $.02 per share, in Q4 2010 was turned into a profit of $263,000, or break-even on a per-share basis, in Q4 2011.

For full-year 2011, Transgenomic saw revenues climb to $32 million, up 60 percent year over year from $20 million in 2010. Clinical Labs revenue came in at $16 million, Diagnostic tools had $13.7 million, and Pharmacogenomics had $2.3 million.

Transgenomic decreased R&D spending 4 percent year over year to $2.2 million from $2.3 million but increased SG&A spending 76 percent to $19.2 million from $10.9 million.

The company had a net loss of $9.8 million, or $.22 per share, compared to a net loss of $3.1 million, or $.06 per share, in 2010. Transgenomic attributed the increase in net loss to an interest expense of $1 million and non-cash charges for preferred-stock valuation of $6.1 million, as well as amortization related to acquired intangibles and stock option expenses.

The firm ended 2011 with $4.9 million in cash and cash equivalents.

In a statement, Transgenomic President and CEO Craig Tuttle said that the year-over-year growth in 2011 reflected improvement in the firm's clinical reference lab and pharmacogenomics lab businesses.

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Transgenomic's Q4 Revenues Increase 69 Percent

Research and Markets: Molecular Diagnostics: Market Segmentation and Opportunities – Emphasis on NGS and Its Emerging …

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DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/aa887c/molecular_diagnost) has announced the addition of the "Molecular Diagnostics: Market Segmentation and Opportunities - 4th Edition" report to their offering.

Molecular diagnostics (MDx) are a class of in vitro diagnostic (IVD) tests that identify nucleic acids, such as DNA. MDx tests may identify nucleic acids that are the genetic material of foreign organisms (e.g., HIV genotyping, MRSA screening) or the genetic markers of an individual patient (e.g., Her-2 overexpression for breast cancer, Factor V Leiden for coagulation). MDx tests continue to be the fastest growing segment within the IVD space, driven by high sensitivity, fast turnaround time, easy workflow and relatively low-cost compared to other techniques, such as culture-based or immune-based tests.

MDx involves platforms and assays that leverage multiple technologies to identify genetic variations. Technologies utilized include; PCR (e.g., HBV qualitative screening; Roche) qPCR (e.g., MRSA screening; Cepheid), TMA (CT/GC screening; Gen-Probe), FISH (PathVysion Her-2; Abbott), capillary electrophoresis (CE) sequencing (e.g., BRAC 1/2 testing; Myriad Genetics), next generation sequencing (Trisomy21 test; Sequenom), microarrays (Amplichip, Roche) and a host of other methods (e.g., pyrosequencing, bDNA, hybrid capture, hybridization beads, kPCR, electrochemical detection).

Analysis from this report indicates that the -$5.9B MDx market (2011E) is expected to grow at >15% p.a. over the next 4 years, reaching $10.9B by 2015. MDx growth is expected to continue to be driven by increased incidence of chronic diseases due to an aging population, increased availability of various tests, and the further adoption of Pharmacogenomics / personalized medicine.

This report reviews the market size, growth, segments and trends of the MDx industry from 2007 through 2015. The market is segmented to provide insights on specific growth opportunities by therapeutic area (infectious diseases, oncology, HPV, others), technology (PCR, qPCR, TMA, hybrid capture, CE Sequencing, NGS, FISH, other), analytes tested (low and high plex level), test rationale (predisposition, screening, diagnosis, therapy selection, monitoring), test location (reference labs, academic hospitals, blood banks, other) and geography (U.S., Europe, Japan, rest of the world). Growth and growth drivers for each segment are quantified and reviewed.

Major competitors shaping the industry include BioPharma (e.g., Abbott, Roche), IVD/MDx pure-play companies (e.g., Myriad Genetics, Cepheid, Gen-probe) or research tool companies (e.g., Illumina, Life Technologies). Major competitors are reviewed along with their key platforms and underlying technologies.

MDx is a highly regulated space. IVD instruments/assays are treated as medical devices and often require 510(k)/IVD clearance to gain full adoption in the marketplace. We briefly review the various level of clearance for MDx tests.

Finally, this report explores opportunities and challenges in the MDx industry. In this fourth edition, we place an emphasis on NGS and its emerging adoption in clinical settings, as well as other emerging technologies (e.g., dPCR, CGH).

Key Topics Covered:

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Research and Markets: Molecular Diagnostics: Market Segmentation and Opportunities - Emphasis on NGS and Its Emerging ...

Will PCORI's Patient-Centered Comparative Effectiveness Research Track with Personalized Rx?

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By Turna Ray

After the Patient-Centered Outcomes Research Institute held a meeting this week to gather public input on its comparative effectiveness research priorities, personalized medicine stakeholders are still uncertain to what degree the institute will fund studies that aim to define how well drugs work in molecularly distinct patient groups or if it will mostly fund research to gauge how interventions work in the general population.

Another unknown as PCORI further defines its CER framework is whether "patient-centered research" a term the institute has been working to define with public input will explicitly mention personalized medicine principles. Whether it does or not could signal whether comparisons of genomic medicine to the standard of care will be a major focus of PCORI's CER efforts.

PCORI, a non-profit organization formed by the 2010 Patient Protection and Affordable Care Act, has issued a draft document outlining the research areas in which it wants to conduct studies comparing the safety and efficacy of medical interventions, healthcare delivery models, and infrastructure. The findings from such CER, PCORI hopes, will help drive informed healthcare decision making, improve patient outcomes, and reduce unnecessary spending in healthcare.

The public was invited to discuss the preliminary research agenda with PCORI and key stakeholders at a meeting this week. PCORI is also accepting written comments on its draft research agenda until March 15.

PCORI is planning to spend $122 million for research activities in 2012, and it's possible that some of this money may go toward funding CER on molecularly targeted personalized medicine products. According to PCORIs statutory purpose, the research the institute supports must consider how disease can be prevented, diagnosed, and treated in patient subpopulations, which could include groups defined by molecular subtypes.

Regardless, some believe that the focus areas outlined in PCORI's draft research agenda are too broad, and personalized medicine principles, which are still new and evolving, can very easily get lost in the mix.

"PCORI was designed to address specific, practical questions of national importance," Amy Miller, vice president of public policy for the advocacy organization Personalized Medicine Coalition, said at the meeting according to prepared comments provided to PGx Reporter. "However, the broad and vague drafting of the research priorities is more appropriate for traditional, investigator-driven research, which may or may not address the types of questions PCORI must answer."

In addition, "since broad drafting does not allow for an examination of individual research proposals, topics, or research questions, it is not possible to say whether PCORIs work will support personalized medicine or not," Miller said.

Since PCORI was formed, the PMC has been trying to remind the institute's leaders that their charge isn't just to look at whether most people respond better to one drug over another, but to investigate how and why treatments work best in some people with a unique set of characteristics. "It is not enough, in the PMCs opinion, to say that one therapy works for most people in the aggregate," Miller said. "To enable personalized medicine, research must explain why a therapy works and for what types of patients."

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Will PCORI's Patient-Centered Comparative Effectiveness Research Track with Personalized Rx?