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Scientists re-imagine how genomes are assembled

Posted on November 26, 2013
University Of Massachusetts Medical School scientists re-imagine how genomes are assembled

3D interaction frequencies can be used to bridge gaps in the DNA sequence and assemble genomes. Credit: Noam Kaplan, PhD, UMass Medical School
Scientists at the University of Massachusetts Medical School (UMMS) have developed a new method for piecing together the short DNA reads produced by next-generation sequencing technologies that are the basis for building complete genome sequences. Job Dekker, PhD, and colleagues have shown that entire genomes can be assembled faster and more accurately by measuring the frequency of interactions between DNA segments and by using their three-dimensional shape as a guide. Employing this technique, they have been able to place 65 previously unaccounted for DNA fragments in incomplete regions of the human genome.

Details of the study appear online in Nature Biotechnology.

“The ability of next-generation sequencing technologies to produce hundreds of millions of short reads of DNA sequences has been an incredible boon for biomedical researchers,” said Dr. Dekker, co-director of the Program in Systems Biology, professor of biochemistry and molecular pharmacology at UMMS and senior author of the study. “As these DNA sequences have become shorter and shorter, however, assembling complete genomes have become increasingly challenging. After 20 years of intense efforts, even the human genome still has gaps.

“Using the 3D structure of the genome as a guide, we have shown that it’s possible for these snippets of DNA sequences to be assembled quickly, cheaply and more accurately than current methodologies allow. This elegant and powerful technique will allow us to complete the human genome, assemble the genomes of any other species and facilitate new genetic discoveries more quickly.”

Read more at: Phys.org

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