Study Helps Pinpoint Genetic Variations In European Americans

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Study Helps Pinpoint Genetic Variations In European Americans

http://www.medicalnewstoday.com/articles/117702.php

An international team of researchers has identified just 200

positions within the curves of the DNA helix that they believe

capture much of the genetic diversity in European Americans, a

population with one of the most diverse and complex historic origins

on Earth. Their findings narrow the search for the elusive ancestral

clues known as single nucleotide polymorphisms, or SNPs, that cause

disease and account for the minute variations in the European

American population.

" With this study, we looked at a very large population to determine

how each individual could be stratified based on his or her DNA, "

said Petros Drineas, assistant professor of computer science at

Rensselaer Polytechnic Institute and one of the two lead authors of

the study. The researchers can now begin to analyze each SNP to

understand the possible biological significance of those genetic,

ancestral differences.

The research, which was published in the July 2008 edition of PLoS

Genetics, is the first to isolate genetic ancestral clues based on a

method that is purely computational, requiring no previous personal

history. The other lead author of the study is Peristera Paschou of

the Democritus University of Thrace in Greece.

The researchers plan to use the data to determine if any of the

approximately 200 ancestry informative SNPs that they have identified

change the way the body develops. " We want to see if the SNPs tied to

a specific ancestry hold any biological significance to populations

of different origins. We want to see if the SNPs that we isolated are

related to natural selection and adaptation, for example to the

weather conditions of different regions, " Drineas said. To help do

so, the research team will move from the computer lab to the biology

lab for further study.

In addition, the researchers hope that their findings will help

narrow down the search for those SNPs that cause disease, according

to Drineas.

Our genes are being increasingly linked to our susceptibility to

certain diseases. Today, scientists are on the prowl to isolate and

understand these " weakest links " in our DNA. With the discovery of

each tiny SNP that is linked to specific diseases, researchers come

closer to understanding our predisposition to certain diseases, as

well as to developing cures.

However, SNPs linked to disease account for only a minuscule fraction

of the estimated 10 million SNPs found in the human genome.

Scientists have made great strides to narrow down the genetic

playfield to just the genetic variations that cause disease, but

other minor genetic variations like ancestry are only recently being

accounted for. With this study, researchers will be able to quickly

and inexpensively identify the genes linked to ancestry and unrelated

to disease, and remove many of them from contention as causes of

disease, thus greatly narrowing the search.

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 ; Caroline M. Nievergelt of the Scripps

Research Institute and the University of California at San Diego;

Deborah A. Nickerson and D. of the University of

Washington; M. Ridker and I. Chasman of Brigham and

Women's Hospital; 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).