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Cold Spring Harbor Lab eyes Sudoku in DNA research

Sudoku, an 81-box numerical sequence puzzle, may be just a coffee-table conundrum to some, but for Cold Spring Harbor scientists it is the guide to hastening the way DNA is coded. Researchers, using the logic of Sudoku, have discovered a method to manipulate the process of genome sequencing they say will save time and money. The study - led by Gregory Hannon, a professor at the Cold Spring Harbor Laboratory, and first authored by Yaniv Erlich, a graduate student there - is the cover story of Wednesday's issue of the journal Genome Research. For a population of thousands of people, the process of determining the order of chemical building blocks through DNA sequencing using conventional methods would take years and could cost $10 million or more, Hannon said. With the "DNA Sudoku" method, scientists can obtain that information in several weeks at a cost of roughly $50,000 to $80,000, he said. "What we developed is a cost-effective method using computational pooling," Erlich said. Using a 2,000-year-old Chinese remainder theorem and applying the rules of Sudoku, Erlich and a team of researchers computed an algorithm that is able to track and process thousands of DNA sequences at once. Using this method, scientists are able to genotype, or sequence, specific areas of the DNA to much more quickly identify diseases such as cystic fibrosis, Tay-Sachs disease and hemophilia, both researchers said. "Now we can take all the samples together, pool them and look at them in different patterns," Erlich said. The Cold Spring Harbor Laboratory is collaborating with Dor Yeshorim, a Brooklyn-based organization geared toward minimizing genetic diseases among Orthodox Jews. Dor Yeshorim has collected DNA from thousands of people to clinically test the proposed method, Erlich said. Scientists within the field have taken notice of the study. "There is an entire field of genetic variation undergoing revolution with higher technology and collection of larger data regarding variants in DNA," said Itsik Pe'er, an assistant professor of computer science at Columbia University who studies, develops and applies computational methods in human genetics. He said he is enthusiastic about "the ability to use this logic in order to increase the efficiency of current technology to access DNA." Erlich said the "DNA Sudoku" has been patented by the lab, and he hopes the new method's speed will be helpful to larger clinical applications such as HLA typing, which is used to determine compatibility of organ donors.

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