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 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).About Rensselaer
Gabrielle DeMarco | Newswise Science News
Self-organising system enables motile cells to form complex search pattern
07.05.2019 | Westfälische Wilhelms-Universität Münster
Mouse studies show minimally invasive route can accurately administer drugs to brain
02.05.2019 | Johns Hopkins Medicine
The quality of additively manufactured components depends not only on the manufacturing process, but also on the inline process control. The process control ensures a reliable coating process because it detects deviations from the target geometry immediately. At LASER World of PHOTONICS 2019, the Fraunhofer Institute for Laser Technology ILT will be demonstrating how well bi-directional sensor technology can already be used for Laser Material Deposition (LMD) in combination with commercial optics at booth A2.431.
Fraunhofer ILT has been developing optical sensor technology specifically for production measurement technology for around 10 years. In particular, its »bd-1«...
The well-known representation of chemical elements is just one example of how objects can be arranged and classified
The periodic table of elements that most chemistry books depict is only one special case. This tabular overview of the chemical elements, which goes back to...
Light can be used not only to measure materials’ properties, but also to change them. Especially interesting are those cases in which the function of a material can be modified, such as its ability to conduct electricity or to store information in its magnetic state. A team led by Andrea Cavalleri from the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg used terahertz frequency light pulses to transform a non-ferroelectric material into a ferroelectric one.
Ferroelectricity is a state in which the constituent lattice “looks” in one specific direction, forming a macroscopic electrical polarisation. The ability to...
Researchers at TU Graz calculate the most accurate gravity field determination of the Earth using 1.16 billion satellite measurements. This yields valuable knowledge for climate research.
The Earth’s gravity fluctuates from place to place. Geodesists use this phenomenon to observe geodynamic and climatological processes. Using...
Discovery by Brazilian and US researchers could change the classification of two species, which appear more akin to jellyfish than was thought.
The tube anemone Isarachnanthus nocturnus is only 15 cm long but has the largest mitochondrial genome of any animal sequenced to date, with 80,923 base pairs....
29.04.2019 | Event News
17.04.2019 | Event News
15.04.2019 | Event News
19.06.2019 | Physics and Astronomy
19.06.2019 | Information Technology
19.06.2019 | Materials Sciences