New approach for efficient analysis of emerging genetic data

September 6, 2012, Roswell Park Cancer Institute

(Medical Xpress)—With the ability to sequence human genes comes an onslaught of raw material about the genetic characteristics that distinguish us, and wading through these reserves of data poses a major challenge for life scientists. Researchers at Roswell Park Cancer Institute (RPCI) and the Center for Human Genome Variation at Duke University Medical Center (DUMC) have developed an approach for analyzing data that can help researchers studying genetic factors in disease to quickly cull out relevant genetic patterns and identify variants that lead to particular disorders.

The researchers outline this new approach in a study published in the September issue of The . They note that while genome-wide association studies (GWASs), which analyze the DNA of many people in order to reveal genetic variations associated with disease, have reported thousands of variants associated with different traits, it's very difficult to isolate "causal variants," those genetic irregularities that appear to indicate the presence of a particular disease.

RPCI biostatician Qianqian Zhu, PhD, Assistant Member of the Department of Biostatistics & Bioinformatics and Director of the Institute's Statistical Genetics & Genomics Resource, began this work as a postdoctoral researcher at Duke and completed the study after joining the Roswell Park faculty. The computational method that she and her collaborators established—which they call the preferential linkage disequilibrium approach—follows variants reported by GWASs, then cross-references those variants with a comprehensive variant catalog generated through robust "next generation" sequencing in order to pinpoint causal variants. For this study, the team looked at DNA from 479 people of European descent.

"To test our method, we ran it on five diseases for which the causal variants are known, and in every case we did identify the real causal variant," notes Zhu, the paper's first author. "We're confident that our method can be applied to genome-wide association studies related to diseases for which there are no known causal variants, and by extension may advance the development of targeted approaches to treating those diseases."

"This approach helps to intergrade the large body of data available in GWASs with the rapidly accumulating sequence data," adds David B. Goldstein, Richard and Pat Johnson Distinguished University Professor and Director of the Center for Human Genome Variation at DUMC and senior author of the paper.

The study, "Prioritizing Genetic Variants for Causality on the Basis of Preferential Linkage Disequilibrium," is available online at www.cell.com/AJHG/abstract/S00 … -9297%2812%2900367-9 .

Explore further: New genetic risk factors of lupus found in study of African-American women

Related Stories

New genetic risk factors of lupus found in study of African-American women

June 24, 2011
Researchers from Boston University's Slone Epidemiology Center have found four new genetic variants in the major histocompatibility complex (MHC) that confer a higher risk of systemic lupus erythemathosus ("lupus") in African ...

Recommended for you

A centuries-old math equation used to solve a modern-day genetics challenge

January 18, 2018
Researchers developed a new mathematical tool to validate and improve methods used by medical professionals to interpret results from clinical genetic tests. The work was published this month in Genetics in Medicine.

Peers' genes may help friends stay in school, new study finds

January 18, 2018
While there's scientific evidence to suggest that your genes have something to do with how far you'll go in school, new research by a team from Stanford and elsewhere says the DNA of your classmates also plays a role.

Epigenetics study helps focus search for autism risk factors

January 16, 2018
Scientists have long tried to pin down the causes of autism spectrum disorder. Recent studies have expanded the search for genetic links from identifying genes toward epigenetics, the study of factors that control gene expression ...

Group recreates DNA of man who died in 1827 despite having no body to work with

January 16, 2018
An international team of researchers led by a group with deCODE Genetics, a biopharmaceutical company in Iceland, has partly recreated the DNA of a man who died in 1827, despite having no body to take tissue samples from. ...

The surprising role of gene architecture in cell fate decisions

January 16, 2018
Scientists read the code of life—the genome—as a sequence of letters, but now researchers have also started exploring its three-dimensional organisation. In a paper published in Nature Genetics, an interdisciplinary research ...

Study advances gene therapy for glaucoma

January 16, 2018
While testing genes to treat glaucoma by reducing pressure inside the eye, University of Wisconsin-Madison scientists stumbled onto a problem: They had trouble getting efficient gene delivery to the cells that act like drains ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.