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California computer scientists double volume of data in NIH biotech repository

iciently deal with different types of data, for instance, unrelated or related individuals." Indeed, for the project, Halperin extended the HAP algorithm to work with 'trios' -- where genotypes are available for a mother, father and their child -- taking into account that haplotypes of the children are copies of the haplotypes of the parents.

As a side effect of their research, the computer scientists are now depositing 15 gigabytes of data into dbSNP, and their article in Genome Research aims to encourage the research community to use the data depository as a scientific resource. Researchers can use these reference data sets as tools to guide their own studies into the genetic basis of common diseases.

To that end, the team's next collaboration with NCBI researchers will be to help design disease-association studies. "If a researcher is interested in a specific gene, we can use all the available data to come up with how to design the experiment," said Eskin. "We can tell how many individuals' genotypes need to be sequenced - and how many and which SNPs to collect - to minimize the cost and processing power needed for the most effective study correlating genetic data and the incidence of disease."

Disease association research is the main reason why the group from Calit2 and ICSI opted to identify tag SNPs across the entire NCBI database and make all of them available to the research community. Said Halperin: "If you are going to perform a disease association study, it's more economical to use these tag SNPs than the entire data."


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Source:University of California - San Diego


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