Rensselaer Research ReviewWinter 2008
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Petros Drineas
Petros Drineas, assistant professor of computer science at Rensselaer and one of the two lead authors of the study
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Advantages of the Computational Method

With this method, the researchers did not need prior information from the participants regarding their ancestry, which is required for most current genetic population studies. “Because this method is purely computational and leverages linear algebraic methods such as Principal Components Analysis, without the use of information on self-reported ancestry, we were able to treat the data as a black box,” Drineas said. Drineas does note that such self-reporting in genetics studies remains a fairly accurate and important way to trace ancestry, but is often difficult in populations as varied as European Americans. 

The European American population was chosen because its genetic background, reflecting its historic origins, is among the most complex on the planet, requiring fine resolution characterization of the genetic code in order to define genetic structure, according to Drineas.

The researchers analyzed 1,521 individuals for more than 300,000 SNPs across the entire genome. The data were made available by the National Institute of Neurological Disorders and Stroke (NINDS) as well as the CAP (Cholesterol and Pharmacogenetics) and PRINCE (Pravastatin Inflammation/CRP Evaluation) studies. The team used linear algebra to find patterns in the highly diverse data. When the data sets were analyzed using the proposed algorithms, these patterns pointed to SNPs shared between groups from the same ancestral background.

“Much of the genetic variation was found to stretch between two ‘points’ — what we speculate is the Northern European to Southern European ancestry axis,” according to Drineas and Paschou. Importantly, their study removes any redundant SNPs uncovered during the modeling process, better targeting the most informative SNPs and reducing genotyping cost. 

Drineas and Paschou were assisted in the research by Rensselaer graduate student Jamey Lewis; Caroline M. Nievergelt of the Scripps Research Institute and the University of California at San Diego; Deborah A. Nickerson and Joshua D. Smith of the University of Washington; Paul M. Ridker and Daniel I. Chasman of Brigham and Women’s Hospital; Ronald M. Krauss of the Children’s Hospital of Oakland Research Institute; and Elad Ziv of the University of California San Francisco. 

The research was funded in part by a National Science Foundation (NSF) CAREER award to Drineas and a grant from the National Institutes of Health (NIH).

 

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