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Genomic Health, NCCN, NIH, Third Wave Technologies, Craig Venter, DiaGenic, Harvard Medical School, Michael J. Fox Foundation, Qiagen, Ventana

Genomic Health's Breast Cancer Test Listed in NCCN's Guidelines
Genomic Health said this week that its predictive breast cancer assay has been included in the National Comprehensive Cancer Network’s 2008 Breast Cancer Treatment Guidelines.
The company’s Oncotype DX is a multi-gene expression test used to predict the chances of breast cancer recurrence and the likelihood that chemotherapy will benefit certain patients, the company said.
NCCN is an alliance of 21 cancer centers aimed at improving care and treatments for cancer patients.
In October another professional group, the American Society of Clinical Oncologists – a group representing 25,000 oncology practitioners and all oncology disciplines – included the test in its guidelines.
Genomic Health officials have said that recommendations from groups such as ASCO, and now NCCN, will improve OncotypeDx’s prospects for reimbursement and encourage physician adoption of the test.

NIH To Award $2M to Study Genetic Variations Linked to HIV Susceptibility and Drug Abuse
The National Institutes of Health is seeking proposals for research projects that will study genetic variations linked to susceptibility for HIV-1 infection and AIDS progression among drug-abusing populations, according to a request for applications NIH issued in late December.
According to the RFA, available here, the National Institute on Drug Abuse plans to disburse up to $2 million between four and seven projects that will study how genetic factors may provide “protection from or vulnerability to infection, and how drugs of abuse, medications for drug addiction, and HIV-1 treatment interact with both host and viral genes.”
NIH said it will also support research into the effects of viral mutations and recombination associated with drug abuse on host responses to infection, as well as the pharmacogenetics of interactions among HIV-1 treatment medications and either drugs of abuse or therapies used in the treatment of drug addiction. 
“A more complete understanding of the molecular mechanisms by which genetic variations provide protection from or vulnerability to infection and disease progression, and how drugs of abuse and medications for drug addiction interact with both host and viral genes is needed,” the NIH said in the RFA.
NIH said it plans to support research using of appropriate in vitro or in vivo models involving individuals chronically using addictive substances “to shed light on our understanding of the role of genetic variation within genes involved in modulating immune function, or genes that are highly expressed in monocyte derived dendritic cells, mucosal cells, or other cells/tissues that may alter an individual’s susceptibility to HIV-1 infection.”
NIH also plans to study whether drugs commonly abused, such as methamphetamines, interact with host or viral genetic factors to either increase HIV-1 susceptibility or diminish a person’s ability to internalize pathogens and subsequently activate T cells. 
Letters of intent are due Feb. 27 and applications are due March 27.

Third Wave Completes Clinical Trial Enrollment for HPV Tests
Third Wave Technologies said late last month that it has completed patient enrollment for a clinical trial involving its two human papillomavirus tests.
The company said it has enrolled 2,000 normal subjects and 1,400 women with atypical Pap test results. Next steps in the clinical trial include obtaining final colposcopy and biopsy data, validating and opening a database, and submitting pre-market approval applications to the US Food and Drug Administration.
The company said it expects to file for FDA approval for two HPV products in the first quarter of 2008. One is a test that will screen for 14 high-risk types of HPV and the other is a test for HPV types 16 and 18, the two most carcinogenic types of the virus.

Venter's Genome, RT-PCR Cancer Dx Score High on Time Magazine 'Top 10' Lists
Craig Venter’s diploid genome sequence was Time magazine’s second-most important “scientific discovery” in 2007, while an RT-PCR-based breast cancer test made by a Johnson & Johnson subsidiary was the second-most important “medical breakthrough” of the year.
Venter’s genome, the first diploid of a known individual, appeared in the September issue of PLoS Biology. In a press briefing announcing the research, which used Sanger sequencing, Venter said it is “probably the first and last” individual genome to be sequenced by the technology because of the “cost and time involved.”
Venter estimated that the project cost at least $70 million. Still, the “high-quality draft” is not yet finished. To close the gaps and improve the assembly of haplotypes, the scientists are now generating additional data using next-generation sequencing technologies.
The US Food and Drug Administration in July cleared an RT-PCR assay that detects the spread of breast cancer in the lymph nodes. The test, made by Johnson & Johnson subsidiary Veridex, was No. 2 on Time magazine’s Top 10 list of “medical breakthroughs.”
The intra-operative test, called the GeneSearch breast lymph node assay, uses real time reverse transcriptase PCR on tissue extracted from a sentinel lymph node tissue sample to detect genes indicating that breast cancer has metastasized into the node.
Conducted on Cepheid’s SmartCycler system, the test can generate results in 35 to 40 minutes compared with the two or three days for standard tissue pathology, Veridex said.
The complete Top 10 Medical Breakthroughs can be seen here.

DiaGenic, Harvard Medical School to Use Michael J. Fox Funds for Parkinson’s Dx Research
DiaGenic and researchers at Harvard Medical School will use funding from the Michael J. Fox Foundation to develop a blood-based test for early detection of Parkinson’s disease.
DiaGenic will work with Clemens Scherzer, an assistant professor of neurology at Brigham and Women’s Hospital and Harvard Medical School, who has led the MJFF-funded Harvard PD Biomarker Study for three years.
The study partners will identify and validate gene expression signatures for Parkinson’s using peripheral blood samples that have already been collected for the Harvard study. Signatures will be incorporated into a test to run on a standard platform that will be combined with DiaGenics’ analysis software.
The grant will cover the initial funding for the study, the company said, but the amount of the gift was not disclosed. 
Scherzer said in a statement that he is “optimistic that the use of peripheral gene expression will prove valuable for the early detection of neurological disorders.”

Qiagen, Ventana Settle IP Litigation
Qiagen and Ventana Medical Systems jointly announced Dec. 20 that they have agreed to settle litigation regarding two expired patents covering human papillomavirus probes.
The firms said that they had mutually agreed to terms on Dec. 15 settling litigation of the expired patents, US Nos. 4,849,331 and 4,849,332.
Under terms of the settlement, Ventana agreed to pay Qiagen an undisclosed sum. In return, Qiagen acknowledged that pursuant to an asset purchase agreement signed Sept. 23, 2002, Ventana has lawfully succeeded to certain rights held by Beckman Coulter under a cross-licensing pact originally entered into between Institut Pasteur and Life Technologies and a separate agreement between Institut Pasteur and Beckman.

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The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.