Method implemented in Golden Helix’s HelixTree® Software considerably increases the ability to identify rare genetic variants.
Bozeman, MT, December 06, 2007 – Golden Helix, Inc. today announced that psychiatric researchers at the Zucker Hillside Hospital, working in collaboration with Golden Helix, Inc., have developed a novel analytic method, termed whole genome homozygosity association (WGHA). Powered by Golden Helix’s HelixTree® Software, WGHA was recently used to identify nine genetic risk factors associated with schizophrenia, a debilitating disease that affects nearly one in every 100 people. Accepted for publication by the prestigious journal, Proceedings of the National Academy of Sciences, the study detailing the methods and findings appeared online December 5, 2007. ›› Read the paper
The past year has seen tremendous advances in medical genetics thanks to a new technology – DNA “microchips” that allow researchers to look at hundreds of thousands of variations across the entire human genome. Typically, these genome-wide association studies (GWAS) have employed a basic analytic approach in which each genetic snippet (called a SNP) is examined one-at-a-time. While this method has led to several important new genes for illnesses ranging from diabetes to cancer, these studies have not yet exploited the full capabilities of the DNA chip technology and are often hindered by false discoveries resulting from simultaneously performing hundreds of thousands of statistical tests.
WGHA differs from standard analysis, in that it simultaneously looks at genetic information derived from the patient’s mother and father, looking for stretches of DNA (called runs of homozygosity (ROH)) that were inherited identically from both. Looking at ROHs rather than single SNPs exploits the correlation structure of high resolution whole genome data, reducing the number of statistical tests performed and increasing the ability to find rare genetic variants.
“Developing WGHA allowed us to look at patterns that emerged across clusters of SNPs, which moved us beyond our prior research” said Todd Lencz, PhD, the first author of the study, and an investigator at Zucker Hillside and The Feinstein Institute for Medical Research. “Even more importantly, the WGHA technique can now be applied to any other illness with a genetic component, potentially locating disease hotspots containing rare variants that might be missed with standard analytic techniques.”
Validation of the new method is demonstrated in part by the fact that four of the nine ROH regions identified in Dr. Lencz’s study contain genes that have been previously associated with schizophrenia. The remaining regions contain newly discovered genes involved with the structure and survival of neurons. These results may improve the ability to diagnose, and ultimately develop new treatments for specific genetic subtypes of schizophrenia.
“We’re constantly seeking to develop and implement new analytical methods to help our customers get more out of today’s information rich high resolution arrays,” affirmed Dr. Christophe Lambert, President and CEO of Golden Helix. “This was a great opportunity to work first hand with Dr. Lencz and his team to develop a novel method that will benefit the genetic research community as a whole.”
About HelixTree Software
HelixTree, the cornerstone application of Golden Helix’s SNP & Variation Suite, is a powerful and flexible system for population-based SNP analysis. With its unique set of conventional and novel analytic tools, HelixTree provides more ways to discover true genetic associations than any other program. HelixTree supports case/control, quantitative trait loci (QTL) and categorical type analysis including several methods for allelic, genotypic, haplotypic, copy number variation, runs of homozygosity, multi-locus, and regression-based association tests.
About The Feinstein Institute for Medical Research
Headquartered in Manhasset, NY, and part of the North Shore-LIJ Health System, The Feinstein Institute for Medical Research is among the top six percent of all institutions that receive funding from the National Institutes of Health. Building on its strengths in neurodegenerative and psychiatric disorders, genomics and human genetics, immunology and inflammation, and oncology and cell biology, its goal is to understand the biological processes that underlie various diseases and translate this knowledge into new tools for diagnosis and treatment. For more information, please visit the Feinstein blog at http://feinsteininstitute.typepad.com/feinsteinweblog/.
About Golden Helix
Founded in 1998, Golden Helix is the global leader in SNP analysis and genetic association software. The company's products are used by hundreds of researchers at the world's top pharmaceutical, biotech and non-profit research organizations and have been cited in nearly 100 peer reviewed publications that detail ground-breaking research for discovering the genetic and environmental basis of disease. Golden Helix is committed to Accelerating the Quest for Significance. For more information, please visit www.goldenhelix.com.
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