Navigation Links
New tool for genome-wide association studies

Modern genotyping technologies offer new opportunities to explore how genes influence health and disease, but also present the challenge of analyzing huge amounts of genetic and clinical data. With this in mind, investigators at the Lausanne Branch of the international Ludwig Institute for Cancer Research (LICR), the Swiss Institute of Bioinformatics (SIB) and the University Hospital of Lausanne have developed AssociationViewer, a computational tool that displays genetic differences between individuals on a large scale. Presented in the March 1st (Vol. 25/5) issue of Bioinformatics, the software is a public resource that will help scientists and physicians discover new genetic markers for diseases and other conditions.

Less than 0.5% of the human genome differs between individuals, but this small fraction holds clues that can reveal how each person will respond to a particular disease, therapy or environmental factor. In the past years, genome-wide association (GWA) studiescomprehensive surveys that look for differences in people's DNA codehave uncovered millions of small genetic variations known as single-nucleotide polymorphisms (SNPs). By sharing GWA data, scientists have gained insight into the genetic basis of many complex diseases including cancer and heart disease, and embarked on developing personalized therapeutics.

According to Dr. Nicolas Guex, a senior bioinformatician at the SIB, those who carry out GWA studies need simple ways to integrate datasets from different sources. They also rely on tools that help them visualize SNPs across the entire map of the genome. "AssociationViewer provides an elegant solution to efficiently mine the wealth of data to generate hypotheses," he says. Another user, Dr. Sam Deutsch at the U.S. Department of Energy Joint Genome Institute, USA, also considers the software to be a powerful tool for computational genetics. "Compared to other tools out there, AssociationViewer brings more flexible integration of external data sources and incorporates novel functionalities for comparing results across different studies." He adds that special features allow users to quickly zoom into relevant regions the genome. "Visualizing significant SNPs in their genomic context is very intuitive," he says.

Dr. Ioannis Xenarios, co-author of the article and Director of the Vital-IT group at the SIB, comments that data sharing remains a challenge for GWA studies, since many scientists still are reluctant to upload their unpublished data on public genome browsers. "AssociationViewer is a way to alleviate data transfer problems and allows people to perform their analyses by tapping into essential external resources. We hope that this tool will deliver new ways to mine complex genomic features."

"The software was developed on the principle that a picture is worth a thousand words," says the study's senior author, Dr. Brian Stevenson at the LICR Lausanne Branch. "It stems from a very successful collaboration between the LICR Computational Genomics Group, the SIB Vital-IT group and researchers who generate association data at the University Hospital of Lausanne, and should prove popular among clinicians, biologists and computer scientists."


Contact: Sarah L. White, Ph.D.
Ludwig Institute for Cancer Research

Related biology news :

1. News from the February 2009 Journal of the American Dietetic Association
2. American Association for Cancer Research hosts Science of Cancer Health Disparities conference
3. American Association for Cancer Research hosts Science of Health Care Disparities Meeting
4. News from the January 2009 Journal of the American Dietetic Association
5. UT faculty members win American Heart Association awards for advancing research
6. 13 UCR faculty members recognized by American Association for the Advancement of Science
7. American Association for the Advancement of Science honors four Iowa Staters
8. American Library Association names NJIT prof’s Whale Music book a top ten
9. News from the December 2008 Journal of the American Dietetic Association
10. American Dietetic Association releases 2008 nutrition trends survey
11. News from the November 2008 Journal of the American Dietetic Association
Post Your Comments:
(Date:10/29/2015)... , Oct. 29, 2015 Today, ... announced a partnership with 2XU, a global leader ... deliver a smart hat with advanced bio-sensing technology. ... other athletes to monitor key biometrics to improve ... strategic partnership, the two companies will bring together the ...
(Date:10/27/2015)... 2015 Munich, Germany ... technology (ASGM) automatically maps data from mobile eye tracking ... , so that they can be quantitatively analyzed with ... Munich, Germany , October 28-29, 2015. SMI,s Automated ... mobile eye tracking videos created with SMI,s Eye ...
(Date:10/26/2015)... , October 26, 2015 ... --> adds Biometrics Market ... 2021 as well as Emerging Biometrics ... reports to its collection of IT ... . --> ...
Breaking Biology News(10 mins):
(Date:11/25/2015)... Nov. 25, 2015  PharmAthene, Inc. (NYSE MKT: PIP) ... a stockholder rights plan (Rights Plan) in an effort ... carryforwards (NOLs) under Section 382 of the Internal Revenue ... PharmAthene,s use of its NOLs could be substantially ... defined in Section 382 of the Code. In general, ...
(Date:11/25/2015)... /PRNewswire/ - Aeterna Zentaris Inc. (NASDAQ:  AEZS; TSX: AEZ) ... remain fundamentally strong and highlights the following developments: ... DSMB recommendation to continue the ZoptEC Phase 3 ... final interim efficacy and safety data , ... with heavily pretreated castration- and Taxane-resistant prostate cancer ...
(Date:11/24/2015)... 24, 2015  Asia-Pacific (APAC) holds the third-largest ... market. The trend of outsourcing to low-cost locations ... higher volume share for the region in the ... margins in the CRO industry will improve. ... ( ), finds that the market earned ...
(Date:11/24/2015)... ... 2015 , ... Copper is an essential micronutrient that all ... copper is also toxic to cells. With a $1.3 million award from the ... a systematic study of copper in the bacteria Pseudomonas aeruginosa (P. aeruginosa), a ...
Breaking Biology Technology: