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California computer scientists double volume of data in NIH biotech repository

Faster computation of haplotypes provides insight into genetic basis of human diseaseHigh-throughput sequencing of an individual's DNA yields a map of genetic variation which can give clues to the genetic underpinning of human disease. The current technologies collect genotypes, or information from the individual's two chromosomes. Yet many scientists believe that drilling down to the variations between individuals' DNA at the level of each chromosome -- so-called haplotypes -- will permit more accurate study of genetic differences and their consequences for medical research and the study of evolution.

Experimental methods for deriving these haplotypes are expensive and time-consuming. But now experts in bioinformatics at two California research institutes have used a different, very fast and relatively low-cost computational tool to 'crunch' the world's largest repository of genotypes to predict their haplotypes -- and they did so in less than 24 hours, approximately 1,000 times faster than the prevailing technology until now. Their findings are featured in a special issue of the journal Genome Research, published today.

"This information provides an invaluable resource for understanding the structure of human genetic variation," said lead author Eleazar Eskin, a professor of computer science and engineering at the University of California, San Diego who is affiliated with the California Institute for Telecommunications and Information Technology (Calit2). "A deeper understanding of the data will improve the design of studies that look for associations between certain genes and disease or inherited conditions."

The team from UCSD and the International Computer Science Institute (ICSI) processed all 286 million human genotypes in the dbSNP database of the National Center for Biotechnology Information (NCBI), part of National Institute of Health's National Library of Medicine. The repository includes all publicly available data on single
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Source:University of California - San Diego


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