Computer Program Traces Ancestry Using Anonymous DNA Samples
Troy, N.Y. — 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
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.
Plot of genetic markers for 255
individuals from four continental regions. Red and green
represents identical genotypes. Black represents
genotypic variations. Notice the distinct patterns formed
in the four continental blocks, highlighting the genetic
similarities between people of the same ancestry.
Image Credit: Democritus University of Thrace/Peristera
“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