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Genetic Association Information Network, Affymetrix, DNAStar, MDS, NimbleGen

Genetic Association Information Network to Use Affy's SNP 6.0 Arrays
The Genetic Association Information Network, a public and private partnership, will use Affymetrix's Genome-Wide Human SNP Array 6.0 in genomic studies of schizophrenia and bipolar disorder, Affy said this week.
GAIN is run by the Foundation for the National Institutes of Health, the National Institutes of Health, and Pfizer Global Research and Development.
Affy said GAIN scientists will use the Human SNP 6.0 to analyze eight thousand samples from various ethnicities.
The company also said the GAIN program will provide information it collects to researchers worldwide through the National Center for Biotechnology Information’s database of Genotype and Phenotype, or dbGaP.
Financial terms of the agreement were not released.
Affy launched the Array 6.0 in late May and is hoping the new chip will help the firm take back some market share from Illumina (see related article).

DNAStar Joins Affymetrix GeneChip Program
DNAStar last week said that its ArrayStar microarray data-analysis software has become compatible with Affymetrix’ Gene Chip microarray platform.
The company now becomes a member of the Affymetrix GeneChip-compatible Applications Program.
DNAStar said the companies will now be able to promote each other’s products through website, training, and promotion channels.

MDS Files to Buy Back Shares
MDS this week filed with the Toronto Stock Exchange to buy back up to 4.5 million of its common shares over the next 12 months.
The potential buyback relates to MDS’ shares that float on the Toronto exchange, and has no bearing on its shares that float on the New York Stock Exchange.
As of June 26, MDS had 122.5 million shares issued and outstanding on the Toronto Stock Exchange.

NimbleGen Among Recipients of NIH Grants for Cancer Genome Atlas Program
Nimblegen Systems this week received a $415,000 grant from the National Institutes of Health to support the development of new technologies for the Cancer Genome Atlas pilot program.
NimbleGen was one of eight recipients of two-year awards from the NIH worth a total of $3.4 million to support the program. The firm, which recently agreed to be acquired by Roche for $272.5 million, will use high-density oligonucleotide arrays to select genomic regions for DNA sequence analysis.
The Cancer Genome Atlas, a joint initiative of the National Cancer Institute and the National Human Genome Research Institute that kicked off in late 2005, aims to "test the feasibility of a large-scale, systematic approach to identifying the changes that occur in the genomes of cancer cells," NIH said in a statement.
"The goal is to generate genomic information that the research community can use to develop new and improved strategies for detecting, treating and, ultimately, preventing cancer," NIH said.
Other than NimbleGen, the following investigators and institutions will use the NIH funds for a number of studies that will generate large amounts of data focused on cancer genomics:
  • Baylor College of Medicine's Aleksandar Milosavljevic will receive $413,000 to develop methods based on next-generation sequencing platforms to investigate structural variations in the genomes of cancer cells.
  • City of Hope/Beckman Research Institute's Gerd Pfeifer will receive $465,000 to study DNA methylation in cancer genomes.
  • Benjamin Tycko, of Columbia University, will receive $443,000 to use high-density oligonucleotide arrays to characterize genomic aberrations and DNA methylation. Timothy Bestor, also at Columbia University, will receive $362,000 to develop methods for high-throughput of DNA methylation.
  • Johns Hopkins University's Andrew Feinberg will use $464,000 to develop new approaches for investigating allele-specific gene expression patterns.
  • Stanford University's Ronald Davis will receive $429,000 to develop methods for high-throughput isolation of genomic regions for DNA sequence analysis.
  • Peggy Farnham of the University of California, Davis, will use $418,000 to develop ChIP-chip assays to study cancer-associated changes in genomic regions that are important in gene regulation, using small fragments of cancer tissue.

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.