Topic Name: Computer Program Traces Ancestry Using Anonymous DNA Samples
Category: Computer science & technology
Research persons: Drineas, Puerto Rico, Greece
Location: Rensselaer Polytechnic Institute (RPI), 110 8th St., Troy, NY 12180, United States
A group of computer scientists, mathematicians, and biologists from around
the world have developed a computer algorithm that can help trace the genetic
ancestry of thousands of individuals in minutes, without any prior knowledge of
their background. The team’s findings will be published in the September 2007
edition of the journal PLoS Genetics.
Unlike previous computer programs of its kind that require prior knowledge of
an individual’s ancestry and background, this new algorithm looks for specific
DNA markers known as single nucleotide polymorphisms, or SNPs (pronounced
snips), and needs nothing more than a DNA sample in the form of a simple cheek
swab. The researchers used genetic data from previous studies to perform and
confirm their research, including the new HapMap database, which is working to
uncover and map variations in the human genome.
“Now that we have found that the program works well, we hope to implement it
on a much larger scale, using hundreds of thousands of SNPs and thousands of
individuals,” said Petros Drineas, the senior author of the study and assistant
professor of computer science at Rensselaer Polytechnic Institute. “The program
will be a valuable tool for understanding our genetic ancestry and targeting
drugs and other medical treatments because it might be possible that these can
affect people of different ancestry in very different ways.”
Understanding our unique genetic makeup is a crucial step to unraveling the
genetic basis for complex diseases, according to the paper. Although the human
genome is 99 percent the same from human to human, it is that 1 percent that can
have a major impact on our response to diseases, viruses, medications, and
toxins. If researchers can uncover the minute genetic details that set each of
us apart, biomedical research and treatments can be better customized for each
individual, Drineas said.
This program will help people understand their unique backgrounds and aid
historians and anthropologists in their study of where different populations
originated and how humans became such a hugely diverse, global society.
Their program was more than 99 percent accurate and correctly identified the
ancestry of hundreds of individuals. This included people from genetically
similar populations (such as Chinese and Japanese) and complex genetic
populations like Puerto Ricans who can come from a variety of backgrounds
including Native American, European, and African.
“When we compared our findings to the existing datasets, only one individual
was incorrectly identified and his background was almost equally close between
Chinese and Japanese,” Drineas said.
In addition to Drineas, the algorithm was developed by scientists from
California, Puerto Rico, and Greece. The researchers involved include lead
author Peristera Paschou from the Democritus University of Thrace in Greece;
Elad Ziv, Esteban G. Burchard, and Shweta Choudhry from the University of
California, San Francisco; William Rodriguez-Cintron from the University of
Puerto Rico School of Medicine in San Juan; and Michael W. Mahoney from Yahoo!
Research in California.
Drineas’ research was funded by his National Science Foundation CAREER award.
Contact: Gabrielle DeMarco
Phone: (518) 276-6542
Rensselaer Polytechnic Institute, founded in 1824, is the nation’s oldest
technological university. The university offers bachelor’s, master’s, and
doctoral degrees in engineering, the sciences, information technology,
architecture, management, and the humanities and social sciences. Institute
programs serve undergraduates, graduate students, and working professionals
around the world. Rensselaer faculty are known for pre-eminence in research
conducted in a wide range of fields, with particular emphasis in biotechnology,
nanotechnology, information technology, and the media arts and technology. The
Institute is well known for its success in the transfer of technology from the
laboratory to the marketplace so that new discoveries and inventions benefit
human life, protect the environment, and strengthen economic development.
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