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Chemo Regimens Selected by MDs: SNP Test to Predict Side Effects

Posted in Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Computational Biology/Systems and Bioinformatics, Genome Biology, Genomic Testing: Methodology for Diagnosis, Health Economics and Outcomes Research, Medical and Population Genetics, Personalized and Precision Medicine & Genomic Research, Population Health Management, Genetics & Pharmaceutical, Technology Transfer: Biotech and Pharmaceutical, tagged chemo regimens, Pathwork Diagnostics, SNP Test on October 16, 2012| 2 Comments »

Reporter: Aviva Lev-Ari, PhD, RN

Inform Genomics Developing SNP Test to Predict Side Effects, Help MDs Choose among Chemo Regimens

October 10, 2012

By Molika Ashford

Inform Genomics, a Boston-based diagnostics company, said its “Oncology Preferences and Risk of Toxicity,” or OnPART, test showed greater than 90 percent accuracy in predicting which cancer patients are at risk of experiencing serious side effects to various chemotherapy regimens in an early-stage study.

The company is developing the test to predict a patient’s risk for six common adverse events to combination chemotherapy regimens for colorectal, breast, lung, or ovarian cancer.

Inform Genomics’ president and CEO, Ed Rubenstein, told PGx Reporter that the company is narrowing down a set of SNP signatures that can predict six common moderate to serious side effects linked to different, but equally effective chemotherapy regimens, including dose-dense doxorubicin, cyclophosphamide and paclitaxel for breast cancer; oxaliplatin-based regimens for colorectal cancer; and carboplatin plus paclitaxel-based regimens for lung and ovarian cancer.

Rubenstein said that results from the discovery study, performed at the West Clinic in Memphis, Tenn., showed the signatures for all six side effects — nausea and vomiting, mouth sores, diarrhea, fatigue, cognitive dysfunction, and peripheral neuropathy — had greater than 90 percent predictive accuracy.

“What’s unique about [OnPART],” he said, “is that [it analyzes] not only genomic risk of six common side effects of combination chemotherapy regimens the way they are actually used in clinical practice, but it also includes a way to quantify patients’ concerns for how they view these side effects,” through a copyrighted patient questionnaire the company calls “Preference Assessment Inventory.”

He explained that Inform Genomics intends the test to display for oncologists the risk of these six side effects across different chemotherapy regimens that are considered “relatively equivalent” from an efficacy standpoint “but have wide variation in their toxicity profile.”

The company hopes this will allow patients to discuss with doctors, before beginning therapy, what their real risks are “as opposed to theoretical risks from population-based studies,” Rubenstein said.

He cited the example of a cancer patient who is a professional musician with a high genetic risk for neuropathy, according to OnPART. This patient’s quality of life would be greatly impacted if the chemotherapy regimen he or she was on caused debilitating nerve damage. “When they fill out their concerns and say neuropathy is a concern for them, that allows the doctor to help them understand their risk, and switch their chemotherapy regimen to another that is equally effective but does not put the patient at risk for neuropathy,” Rubenstein explained.

In the company’s discovery study, researchers tested saliva from 384 patients at the West Clinic who had been followed for a minimum of two cycles of chemotherapy and who had reported symptoms of the six side effects using a validated questionnaire.

Using Illumina microarrays, the group profiled 2.5 million potential SNPs to find those that correlated with particular side effects and regimens. Then the team used Inform Genomics’ proprietary Bayesian analysis algorithms to look at interactions between these SNPs.

“We have list of SNPs, and then from that we look at location on genes or outside genes and look at functional pathways and biology to make sure that what we are looking at makes sense,” Rubenstein explained.

Though the exact number of SNPs to be used for each side effect-predictor in OnPART has not yet been determined, Rubenstein said the marketed panel would likely include about 400 SNPs.

“[Our] commercial product is likely to be a custom chip because we don’t need 2.5 million once we’ve narrowed down the predictive SNPs,” he said. “So, let’s say we have six symptoms and each have 80 to 100 SNPs; maybe the chip would be 400 SNPs.”

The company plans to release a more detailed picture of the study and its results at future oncology meetings.

Rubenstein said the next step will be to raise additional capital and then design prospective validation studies for both OnPART and another test the company is developing to predict oral and gastrointestinal mucositis: side effects of high-dose chemotherapy administered before autologous stem cell transplant for multiple myeloma, Hodgkin’s disease, and non-Hodgkin’s lymphoma.

He said Inform Genomics is currently “in dialogue” with large practices and oncology networks who may be part of these future validation efforts.

“Our current plan is that we would launch the [OnPART] product by the third quarter of 2014,” he said. According to the company’s website, the transplant test would follow in 2015.

Molika Ashford is a GenomeWeb contributing editor and covers personalized medicine and molecular diagnostics. E-mail her here.

Sequenom Center for Molecular Medicine diagnostic services: MaterniT21 Plus test detects for T18 and T13.

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Genome Biology, Genomic Testing: Methodology for Diagnosis, Health Economics and Outcomes Research, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Pharmaceutical R&D Investment, Population Health Management, Genetics & Pharmaceutical, tagged Coventry Health Care, Down syndrome, Molecular Medicine, Pathwork Diagnostics, Sequenom, T13, T18, T21, Tufts University on August 15, 2012| Leave a Comment »

Tufts Health Plan to Cover Sequenom’s MaterniT21, Pathwork’s Tissue of Origin Tests

Reporter: Aviva Lev-Ari, PhD, RN

http://www.genomeweb.com/mdx/tufts-health-plan-cover-sequenoms-maternit21-pathworks-tissue-origin-tests

August 06, 2012

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Tufts Health Plan will begin covering Sequenom’s MaterniT21 Plus trisomy 21 test and Pathwork Diagnostics‘ Tissue of Origin test starting Oct. 1.

In an update to providers posted on its website, the health plan said that it may authorize coverage of the MaterniT21 test for patients who are plan members if they are at least 35 years old when they give birth; have a fetal aneuploidy screening test result including maternal serum screening and/or ultrasound evaluation that indicates the possibility of trisomy 21; or the plan member has a family history or prior pregnancy involving aneuploidy.

In a research note Oppenheimer analyst David Ferreiro said that Tufts Health Plan has approximately 1 million lives under coverage and a network of 90 hospitals and 25,000 healthcare providers.

“We view this decision as an incremental positive for [Sequenom] and as validation of the value proposition MaterniT21 presents to payors,” he said. “The adoption rate is encouraging and could positively impact payor decisions, further entrenching,” the company.

Two weeks ago, Sequenom said that in the second quarter revenues from its Sequenom Center for Molecular Medicine diagnostic services rose five-fold to $8.1 million driven by the MaterniT21 Plus test, which was launched in the fall. The test also detects for T18 and T13.

As adoption of the test continues to ramp at an increasing rate, the San Diego-based company increased its internal goal of billed MaterniT21 Plus tests for 2012 to 50,000 from an earlier goal of 40,000.

The company has stopped announcing coverage decisions by individual plans following an incident in the spring in which Coventry Health Care National Networkterminated a coverage decision for MaterniT21 Plus one week after Sequenom said that Coventy would cover the test. Sequenom said at the time that Coventry’s decision was without cause and was not a judgment on the company, Sequenom CMM, or its products.

In a statement today to GenomeWeb Daily News, a Sequenom spokesperson declined to disclose the terms of the contract with Tufts Health Plan. She said that Sequenom CMM has more than 26 million live under contract, and “we operate as an out-of-network laboratory where we are not yet contracted and bill payors accordingly.”

Tufts Health Plan also said that it will begin coverage of Pathwork Diagnostics’ Pathwork Tissue of Origin test, beginning on Oct. 1. The test is for the identification of challenging tumors, including poorly differentiated, undifferentiated, and metastatic cancers.

The plan said it may authorize coverage of the test if it is ordered by an oncologist and the plan member is diagnosed with metastatic cancer; the clinical evaluation has not identified the primary site of the cancer; the pathology report is submitted to Tufts Health Plan for review; and the pathology examination is unable to conclusively identify the primary site, or has identified two or more possible primary sites.

Use of the test to confirm a diagnosis will not be covered by the health plan.