Navigation Links
New method developed for ranking disease-causal mutations within whole genome sequences
Date:2/7/2014

Seattle, Wash. and Huntsville, Ala.Researchers from the University of Washington and the HudsonAlpha Institute for Biotechnology have developed a new method for organizing and prioritizing genetic data. The Combined AnnotationDependent Depletion, or CADD, method will assist scientists in their search for disease-causing mutation events in human genomes.

The new method is the subject of a paper titled "A general framework for estimating the relative pathogenicity of human genetic variants," published in Nature Genetics.

Current methods of organizing human genetic variation look at just one or a few factors and use only a small subset of the information available. For example, the Encyclopedia Of DNA Elements, or ENCODE, catalogs various types of functional elements in human genomes, while sequence conservation looks for similar or identical sequences that have survived across different species through hundreds of millions of years of evolution. CADD brings all of these data together, and more, into one score in order to provide a ranking that helps researchers discern which variants may be linked to disease and which ones may not.

"CADD will substantially improve our ability to identify disease-causal mutations, will continue to get better as genomic databases grow, and is an important analytical advance needed to better exploit the information content of whole-genome sequences in both clinical and research settings," said Gregory M. Cooper, Ph.D., faculty investigator at HudsonAlpha and one of the collaborators on CADD.

The goal in developing the new approach was to take the overwhelming amount of data available and distill it down into a single score that can be more easily evaluated by a researcher or clinician. To accomplish that, CADD compares and contrasts the properties of 15 million genetic variants separating humans from chimpanzees with 15 million simulated variants. Variants observed in humans have survived natural selection, which tends to remove harmful, disease-causing variants, while simulated variants are not exposed to selection. Thus, by comparing observed to simulated variants, CADD is able to identify those properties that make a variant harmful or disease-causing. C scores have been pre-computed for all 8.6 billion possible single nucleotide variants and are freely available for researchers.

"We didn't know what to expect," Cooper said, "but we were pleasantly surprised that CADD was able not only to be applicable to mutations everywhere in the genome but in fact do a substantially better job in nearly every test that we performed than other metrics."

The CADD method is unique from other algorithms in that it assigns scores to mutations anywhere in human genomes, not just the less-than two percent that encode proteins (the "exome"). This unique attribute will be crucial as whole-genome sequencing becomes routine in both clinical and research settings.


'/>"/>
Contact: Beth Pugh
bpugh@hudsonalpha.org
256-975-3414
HudsonAlpha Institute for Biotechnology
Source:Eurekalert

Related biology news :

1. New 3-D stem cell culture method published in JoVE
2. New methods for better purification of wastewater
3. More effective method of imaging proteins
4. New method for estimating parameters may boost biological models
5. New paper by Notre Dame researchers describes method for cleaning up nuclear waste
6. Scientists discover new method of proton transfer
7. Oceanographers develop method for measuring the pace of life in deep sediments
8. Notre Dame researchers using novel method to combat malaria drug resistance
9. Rapid method of assembling new gene-editing tool could revolutionize genetic research
10. Scientists advance field of research with publication of newly validated method for analyzing flavanols in cocoa
11. Chemical engineers at UMass Amherst find high-yield method of making xylene from biomass
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:2/2/2016)... 2, 2016  Based on its recent analysis ... recognizes US-based Intelligent Retinal Imaging Systems (IRIS) with ... for New Product Innovation. IRIS, a prominent cloud-based ... America , is poised to set the ... retinopathy market. The IRIS technology presents superior price-performance ...
(Date:1/27/2016)... CHESTER, Ohio , Jan. 27, 2016  Rite ... supplier based in West Chester, Ohio ... their award winning service staff, based in ... technical capacity and ability to provide modifications, installations and ... John Dovalina , CEO of PLUS, commented, "PLUS has ...
(Date:1/21/2016)... 21, 2016 --> ... market research report "Emotion Detection and Recognition Market by Technology ... (Facial Expression, Voice Recognition and Others), Services, Application ... to 2020", published by MarketsandMarkets, the global Emotion ... USD 22.65 Billion by 2020, at a CAGR ...
Breaking Biology News(10 mins):
(Date:2/12/2016)... PA (PRWEB) , ... February 12, 2016 , ... ... at the Georgia World Congress Center in Atlanta, Georgia, will include 848 exhibitors ... These leading companies will be displaying products and services used by the scientific ...
(Date:2/11/2016)... NBIX ) today announced its financial results for the quarter ... --> For the fourth quarter of 2015, the ... per share, compared to a net loss of $19.4 million, or ... the year ended December 31, 2015, the Company reported a net ... to a net loss of $60.5 million, or $0.81 loss per ...
(Date:2/11/2016)... ATLANTA , Feb. 11, 2016  Wellcentive ... a Portland, Oregon -based community ... to provide population health analytics, quality reporting and ... help FamilyCare strengthen its team of quality managers, ... reporting to the provider groups serving FamilyCare members. ...
(Date:2/11/2016)... Buffalo, New York (PRWEB) , ... February 11, ... ... and analytical instruments for more than 150 years, continues today to pursue the ... to its line of analytical instruments: the AR9 Refractometer and the AR5 Refractometer. ...
Breaking Biology Technology: