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Affymetrix, Avesthagen, Fred Hutchinson Cancer Research, NSB Postech, USDA

Avesthagen to Use Affymetrix Microarrays in Parsi Study
Affymetrix said this week that Avesthagen will use its microarrays in a genetic study of the Parsi-Zoroastrian population.
Bangalore, India-based Avesthagen plans to conduct a study, called the AvestaGenome Project, of more than 60,000 Parsi individuals in an effort to reveal the genetic basis of longevity among that population. According to the companies, 31 percent of the Parsi population lives beyond the age of 60 compared to 7 percent nationally in India.
Avesthagen researchers intend to correlate genes with longevity, as well as neurodegenerative conditions, breast cancer, diabetes, and other complex diseases in the Parsi community.
The genotyping phase of the project began in October 2007. By the middle of this year, Avesthagen plans to perform gene-expression profiling and transcript mapping experiments across a subset of samples. The project is scheduled to finish by 2013.
Financial terms of the agreement were not disclosed.

Fred Hutchinson, NSB Partner on Protein Microarray Research
Fred Hutchinson Cancer Research Center last week announced that it is collaborating with South Korea-based NSB Postech to study protein microarrays.
The partners are coordinating efforts to determine the efficacy of NSB’s NanoCones surface technology in creating proteomic microarrays, which will be used to study human diseases, the Hutchinson Center said. The collaboration will include a comparison of slides created with NSB’s technology with current industry standard technology.
“We hope this will make our antibody arrays more sensitive and accurate,” Paul Lampe, a member of the Hutchinson Center’s Public Health Sciences Division and associate program head of molecular diagnostics, said in a statement.
NSB will fund the collaboration. Further terms of the alliance were not disclosed.

USDA Scientists Use $3M to Create Soy SNP Library
Researchers with the US Department of Agriculture plan to create a library of 50,000 SNPs from the soybean genome that could be used to develop soybeans with improved yield, greater resistance to pests, and improved protein and oil quality, the USDA’s Agricultural Research Service said late last week.
Scientists at the ARS’ Soybean and Genomics Improvement Research Unit in Beltsville, Md., will be working with $2.9 million in funding from the United Soybean Board.
The researchers will use the SNPs in conjunction with data from the draft of the whole-genome sequencing of the soybean that the US Department of Energy’s Joint Genome Institute completed in January.
The USDA said it is particularly interested in using this data to identify plants carrying traits such as resistance to pests and the production of high-quality oil.
Earlier this month, the agricultural company Monsanto and a Nematode-focused genomics company called Divergence said they had completed a draft of the genome of the soybean cyst nematode.
“This genomics project will greatly aid soybean-breeding efforts,” United Soybean Board Chairman Ike Boudreaux said in a statement. “Ultimately, improved varieties will be available to farmers much faster,” Boudreaux said.
“Our overall goal is to harness the remarkable recent developments in rapid genome analysis to construct a new, highly detailed, high-resolution description of the genetic diversity contained within soybean and its close wild relatives,” ARS administrator Edward Knipling said in the same statement.
Knipling also said that the knowledge the project generates “may serve as a road map for constructing the shortest, most efficient pathways to identifying soybean genes, their functions and their variants.”

The USB also said that the American Soybean Association is supporting the project by lobbying for more federal funding in soybean genomics.

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.