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Researchers to Use Illumina's Omni1-Quad BeadChips in New Genotype Tissue-Expression Project

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This story has been updated to include additional comments from the NIH.

By Justin Petrone

Researchers will use Illumina's Omni1-Quad BeadChips to genotype samples as part of the National Institutes of Health's new Genotype Tissue-Expression project, BioArray News has learned.

The NIH has issued nearly $21 million in grants to support a pilot project for the endeavor, which it announced last week. The project, dubbed GTEx, aims to create a resource of genotype and expression data that researchers can use to study inherited susceptibility to illness. As part of the project, the NIH will also establish a tissue bank for future biological studies.

GTEx seeks to combine genotype and gene expression data "to study systematically how gene expression is regulated in different organs in the human body," the NIH said in a statement. "This would be a key step to explain the underlying biology of many organ-specific diseases."

The two-year pilot phase of the project will include funding for three biospecimen source sites and a lab and data analysis-coordinating center located at the Broad Institute. The biospecimen source sites will be led by the National Cancer Institute's cancer Human Biobank initiative and will be responsible for recruiting donors and collecting tissues.

GTEx's first phase will test the feasibility of collecting high-quality RNA for gene-expression studies from 30 to 50 tissue sites in the body, including the brain, lungs, heart, and muscle.

The sample tissues will come from around 160 deceased donors who were identified through autopsy or organ and tissue transplant programs; a small group of normal tissues from living surgery patients will be used as a control group.

The researchers will collect extensive clinical and medical information from all donors, and each donor's DNA will be genotyped, RNA sequenced, and catalogued for their gene variants, the NIH said.

Jeff Struewing, program director of the GTEx project at the National Human Genome Research Institute, told BioArray News this week that the Broad Institute will use the Omni1-Quad BeadChips to carry out the genotyping portion of the project.

Illumina launched the Omni1-Quad last year (BAN 5/19/2009). The first in the vendor's Omni family of chips, the Omni1-Quad includes SNP content from the 1000 Genomes Project and more than 11,000 copy number variants from the Wellcome Trust Sanger Institute, the Hospital for Sick Children in Toronto, Harvard Medical School/Brigham and Women's Hospital, and Decode Genetics.

The NIH awarded $11.4 million to the Broad Institute to support it in its role as the project's data analysis-coordinating center. The Broad contract will support all the laboratory analyses for GTEx, and basic statistical analysis, Struewing said.

He added that it has not yet been determined how GTEx will use microarrays in addition to next-generation sequencing to generate the expression data in the project.

"The current plan calls for Affymetrix expression arrays on up to 480 samples, but this is quite tentative, in that as the cost of RNA-seq and arrays continue to converge," Struewing said.

Grants funding the biospecimen source sites include $3.5 million for the National Disease Research Interchange in Philadelphia; $2 million to the Roswell Park Cancer Institute in Buffalo, NY; $750,000 to Science Care in Phoenix; and $362,000 to the Brain Endowment Bank at the University of Miami.

NDRI also will collaborate with researchers at Virginia Commonwealth University, which received $283,000.

Grants aimed at helping to develop statistical methods and data-analysis tools include $642,000 to the University of Chicago, which will study ways to use the transcriptome for SNPs and gene annotation; $662,000 to the University of Geneva, which will try to develop methods for high-resolution analysis of genetic effects on gene expression; $594,000 to Harvard University, which will study epistatic and cross-tissue analysis for human gene-expression traits; $676,000 to the University of Chicago for statistical analysis research; and $659,000 to the University of North Carolina at Chapel Hill to help GTEx analyze the relationship between diseases, genes, and the environment.

The National Center for Biotechnology Information will also play a role in GTEx by establishing a database to allow users to view and download computed GTEx results, and provide a controlled-access system for de-identified individual-level genotype, expression, and clinical data through its database of Genotypes and Phenotype. Other genome browsers will also be supported to integrate and display GTEx data, NIH added.

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