Bozeman, Mont and Houston Texas (May 20, 2011) — Though two of the best-known methods for analyzing rare variants in sequencing data were published in 2008 and 2010, they have never been available to the public as a supported package.
Baylor College of Medicine and Golden Helix announce the availability of the Combined Multivariate and Collapsing (CMC) and the Kernel Based Adaptive Cluster (KBAC) methods in Golden Helix’ flagship product, SNP & Variation Suite (SVS).
CMC and KBAC were developed under the direction of Suzanne Leal, PhD, a professor in Baylor’s Department of Molecular and Human Genetics, and are powerful and flexible methods of analyzing rare DNA sequence variants. Leal’s methods allow researchers to assess the combined effect of multiple independent rare and common sequence variants on disease phenotypes. Rare variants are hypothesized to have greater effect sizes than common ones for some diseases, but standard GWAS methodologies that test each variant individually lack sufficient statistical power to detect these associations.
Christophe Lambert, President and CEO of Golden Helix, explained, “The move to next-generation sequencing and the study of rare variants has caused us to rethink analytically how best to assess the effect of genetic variation on disease. The standard methods to analyze common variants in GWAS data are underpowered to test for rare variant complex trait associations. Dr. Leal's methods open exciting opportunities for researchers to statistically explore the importance of rare variants, in addition to common variants, and the role they play on disease.”
The SVS integration of CMC and KBAC is the first supported implementation available in any form, whether free, open-source, or commercial. Furthermore, Golden Helix and Baylor worked together to extend both the CMC and KBAC methods beyond the original paper’s specifications, creating a version that leverages a regression framework. The regression-based adaptations allow users to correct for confounding variables that might otherwise result in spurious results.
“Golden Helix’ integration of CMC and KBAC demonstrates their commitment to working with academia to make cutting edge methodologies available to researchers studying the genetic causes of disease and other traits,” said Dr. Leal. “I am very happy with their implementation of our methods and look forward to working with Golden Helix further.”
SVS is a powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale, complex genomic data.
About Baylor College of Medicine
Baylor College of Medicine (www.bcm.edu) in Houston is recognized as a premier academic health science center and is known for excellence in education, research and patient care. It is the only private medical school in the greater southwest and is ranked as one of the top 25 medical schools for research in U.S. News & World Report. BCM is listed 13th among all U.S. medical schools for National Institutes of Health funding, and No. 2 in the nation in federal funding for research and development in the biological sciences at universities and colleges by the National Science Foundation. Located in the Texas Medical Center, BCM has affiliations with eight teaching hospitals. Currently, BCM trains more than 3,000 medical, graduate, nurse anesthesia, and physician assistant students, as well as residents and post-doctoral fellows. BCM is also home to the Baylor Clinic, an adult clinical practice that includes advanced technologies for faster, more accurate diagnosis and treatment, access to the latest clinical trials and discoveries, and groundbreaking healthcare based on proven research.
About Golden Helix
Golden Helix is a leading bioinformatics organization, specializing in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Our innovative technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine. Used by hundreds of researchers at the world's top pharmaceutical, biotech, and academic research organizations, Golden Helix products and services have been cited in over 500 peer-reviewed publications.
Golden Helix, Inc.