Featured Research

from universities, journals, and other organizations

New Approach Improves Prioritization Of Disease-associated SNPs

Date:
December 5, 2008
Source:
Genome Biology
Summary:
The more often a gene is differentially expressed, the more likely it is to contain disease-associated DNA variants. New research in Genome Biology shows how a list of SNPs in genes that are repeatedly implicated across many publicly-available gene expression microarray experiments (so-called, 'fitSNPs'), based on differential expression rates, can be used to successfully prioritize candidate genes for further research.

The more often a gene is differentially expressed, the more likely it is to contain disease-associated DNA variants. Research published today in BioMed Central's open access journal Genome Biology shows how a list of SNPs in genes that are repeatedly implicated across many publicly-available gene expression microarray experiments (so-called, 'fitSNPs'), based on differential expression rates, can be used to successfully prioritize candidate genes for further research.

Atul Butte from Stanford University School of Medicine, USA, led a team of researchers who developed the new way to prioritize candidate SNPs from genome-wide association studies (GWAS). He said, "fitSNPs successfully distinguished true disease genes from false positives in genome-wide association studies looking at multiple diseases, and can serve as a powerful and convenient tool to prioritize disease genes from this type of study."

The hypothesis that there is an association between gene expression and disease-associated variants has never before been demonstrated with such clarity and at this global scale. The authors have robustly demonstrated that the likelihood of having variants associated with disease was 12 times higher among differentially expressed genes compared to constantly expressed genes.

According to Butte, "As a case study, we looked at type 1 diabetes mellitus. We derived a list of fitSNPs to analyze the top seven loci of the Wellcome Trust Case Control Consortium type 1 diabetes mellitus (T1DM) genome-wide association studies. We then rediscovered all T1DM genes, and predicted a novel gene for a previously unexplained locus."

There are many candidate gene and SNP prioritization methods, and while the authors acknowledge that no single method is perfect, they suggest that using fitSNPs in a complementary fashion with other prioritization methods will significantly lower experimental costs.


Story Source:

The above story is based on materials provided by Genome Biology. Note: Materials may be edited for content and length.


Journal Reference:

  1. Rong Chen, Alex A Morgan, Joel Dudley, Tarangini Deshpande, Li Li, Keiichi Kodama, Annie P Chiang and Atul J Butte. FitSNPs: Highly differentially expressed genes are more likely to have variants associated with disease. Genome Biology, (in press)

Cite This Page:

Genome Biology. "New Approach Improves Prioritization Of Disease-associated SNPs." ScienceDaily. ScienceDaily, 5 December 2008. <www.sciencedaily.com/releases/2008/12/081205094517.htm>.
Genome Biology. (2008, December 5). New Approach Improves Prioritization Of Disease-associated SNPs. ScienceDaily. Retrieved August 27, 2014 from www.sciencedaily.com/releases/2008/12/081205094517.htm
Genome Biology. "New Approach Improves Prioritization Of Disease-associated SNPs." ScienceDaily. www.sciencedaily.com/releases/2008/12/081205094517.htm (accessed August 27, 2014).

Share This




More Health & Medicine News

Wednesday, August 27, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Predicting Heart Transplant Rejection With a Blood Test

Predicting Heart Transplant Rejection With a Blood Test

Ivanhoe (Aug. 27, 2014) Now a new approach to rejection of donor organs could change the way doctors predict transplant rejection…without expensive, invasive procedures. Video provided by Ivanhoe
Powered by NewsLook.com
Better Braces That Vibrate

Better Braces That Vibrate

Ivanhoe (Aug. 27, 2014) The length of time you have to keep your braces on could be cut in half thanks to a new device that speeds up the process. Video provided by Ivanhoe
Powered by NewsLook.com
Smartphone App Tracks Your Heart Rate

Smartphone App Tracks Your Heart Rate

Ivanhoe (Aug. 27, 2014) A new app that can track your heart rate 24/7 is available for download in your app store and its convenience could save your life. Video provided by Ivanhoe
Powered by NewsLook.com
Stroke in Young Adults

Stroke in Young Adults

Ivanhoe (Aug. 27, 2014) A stroke can happen at any time and affect anyone regardless of age. This mother chose to give her son independence and continue to live a normal life after he had a stroke at 18 years old. Video provided by Ivanhoe
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