Featured Research

from universities, journals, and other organizations

Boosting the powers of genomic science

Date:
April 25, 2013
Source:
University of California, San Diego Health Sciences
Summary:
Scientists describe novel statistical models that more broadly and deeply identify associations between bits of sequenced DNA called single nucleotide polymorphisms or SNPs and say lead to a more complete and accurate understanding of the genetic underpinnings of many diseases and how best to treat them.

As scientists probe and parse the genetic bases of what makes a human a human (or one human different from another), and vigorously push for greater use of whole genome sequencing, they find themselves increasingly threatened by the unthinkable: Too much data to make full sense of.

In a pair of papers published in the April 25, 2013 issue of PLOS Genetics, two diverse teams of scientists, both headed by researchers at the University of California, San Diego School of Medicine, describe novel statistical models that more broadly and deeply identify associations between bits of sequenced DNA called single nucleotide polymorphisms or SNPs and say lead to a more complete and accurate understanding of the genetic underpinnings of many diseases and how best to treat them.

"It's increasingly evident that highly heritable diseases and traits are influenced by a large number of genetic variants in different parts of the genome, each with small effects," said Anders M. Dale, PhD, a professor in the departments of Radiology, Neurosciences and Psychiatry at the UC San Diego School of Medicine. "Unfortunately, it's also increasingly evident that existing statistical methods, like genome-wide association studies (GWAS) that look for associations between SNPs and diseases, are severely underpowered and can't adequately incorporate all of this new, exciting and exceedingly rich data."

Dale cited, for example, a recent study published in Nature Genetics in which researchers used traditional GWAS to raise the number of SNPs associated with primary sclerosing cholangitis from four to 16. The scientists then applied the new statistical methods to identify 33 additional SNPs, more than tripling the number of genome locations associated with the life-threatening liver disease.

Generally speaking, the new methods boost researchers' analytical powers by incorporating a priori or prior knowledge about the function of SNPs with their pleiotrophic relationships to multiple phenotypes. Pleiotrophy occurs when one gene influences multiple sets of observed traits or phenotypes.

Dale and colleagues believe the new methods could lead to a paradigm shift in CWAS analysis, with profound implications across a broad range of complex traits and disorders.

"There is ever-greater emphasis being placed on expensive whole genome sequencing efforts," he said, "but as the science advances, the challenges become larger. The needle in the haystack of traditional GWAS involves searching through about one million SNPs. This will increase 10- to 100-fold, to about 3 billion positions. We think these new methodologies allow us to more completely exploit our resources, to extract the most information possible, which we think has important implications for gene discovery, drug development and more accurately assessing a person's overall genetic risk of developing a certain disease."


Story Source:

The above story is based on materials provided by University of California, San Diego Health Sciences. Note: Materials may be edited for content and length.


Journal References:

  1. Andrew J. Schork, Wesley K. Thompson, Phillip Pham, Ali Torkamani, J. Cooper Roddey, Patrick F. Sullivan, John R. Kelsoe, Michael C. O'Donovan, Helena Furberg, Nicholas J. Schork, Ole A. Andreassen, Anders M. Dale. All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs. PLoS Genetics, 2013; 9 (4): e1003449 DOI: 10.1371/journal.pgen.1003449
  2. Ole A. Andreassen, Wesley K. Thompson, Andrew J. Schork, Stephan Ripke, Morten Mattingsdal, John R. Kelsoe, Kenneth S. Kendler, Michael C. O'Donovan, Dan Rujescu, Thomas Werge, Pamela Sklar, J. Cooper Roddey, Chi-Hua Chen, Linda McEvoy, Rahul S. Desikan, Srdjan Djurovic, Anders M. Dale. Improved Detection of Common Variants Associated with Schizophrenia and Bipolar Disorder Using Pleiotropy-Informed Conditional False Discovery Rate. PLoS Genetics, 2013; 9 (4): e1003455 DOI: 10.1371/journal.pgen.1003455

Cite This Page:

University of California, San Diego Health Sciences. "Boosting the powers of genomic science." ScienceDaily. ScienceDaily, 25 April 2013. <www.sciencedaily.com/releases/2013/04/130425213754.htm>.
University of California, San Diego Health Sciences. (2013, April 25). Boosting the powers of genomic science. ScienceDaily. Retrieved July 23, 2014 from www.sciencedaily.com/releases/2013/04/130425213754.htm
University of California, San Diego Health Sciences. "Boosting the powers of genomic science." ScienceDaily. www.sciencedaily.com/releases/2013/04/130425213754.htm (accessed July 23, 2014).

Share This




More Health & Medicine News

Wednesday, July 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Stone Fruit Listeria Scare Causes Sweeping Recall

Stone Fruit Listeria Scare Causes Sweeping Recall

Newsy (July 22, 2014) The Wawona Packing Company has issued a voluntary recall on the stone fruit it distributes due to a possible Listeria outbreak. Video provided by Newsy
Powered by NewsLook.com
Huge Schizophrenia Study Finds Dozens Of New Genetic Causes

Huge Schizophrenia Study Finds Dozens Of New Genetic Causes

Newsy (July 22, 2014) The 83 new genetic markers could open dozens of new avenues for schizophrenia treatment research. Video provided by Newsy
Powered by NewsLook.com
CDC Head Concerned About a Post-Antibiotic Era

CDC Head Concerned About a Post-Antibiotic Era

AP (July 22, 2014) Sounding alarms about the growing threat of antibiotic resistance, CDC Director Tom Frieden warned Tuesday if the global community does not confront the problem soon, the world will be living in a devastating post-antibiotic era. (July 22) Video provided by AP
Powered by NewsLook.com
Courts Conflicted Over Healthcare Law

Courts Conflicted Over Healthcare Law

AP (July 22, 2014) Two federal appeals courts issued conflicting rulings Tuesday on the legality of the federally-run healthcare exchange that operates in 36 states. (July 22) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins