A new computational method has been shown to quickly assign, order and orient DNA sequencing information along entire chromosomes. The method may help overcome a major obstacle that has delayed progress in designing rapid, low-cost -- but still accurate -- ways to assemble genomes from scratch. Data gleaned through this new method can also validate certain types of chromosomal abnormalities in cancer, research findings indicate.
The advance was reported in Nature Biotechnology by several University of Washington scientists led by Dr. Jay Shendure, associate professor of genome sciences.
Existing technologies can quickly produce billions of "short reads" of segments of DNA at very low cost. Various approaches are currently used to put the pieces together to see how DNA segments line up to form larger stretches of the genetic code.
However, current methods produce a highly fragmented genome assembly, lacking long-range information about what sequences are near what other sequences, making further biological analysis difficult.
"Genome science has remained remarkably distant from routinely assembling genomes to the standards set by the Human Genome Project," said the researchers. They noted that the Human Genome Project tapped into many different techniques to achieve its end result. Many of these are too expensive, technically difficult, and impractical for large-scale initiatives such as the Genome 10K Project, which aims to sequence and assemble the genomes of 10,000 vertebrate species.
Members of the Shendure lab that developed what they hope will be a more scalable strategy were Joshua N. Burton, Andrew Adey, Rupali P. Patwardhan, Ruolan Qiu, and Jacob O. Kitzman.
To more completely assemble genomes, they tapped into a technology called Hi-C, which measures the three-dimensional architecture and physical territories of chromosomes within the nuclei of cells. Hi-C maps the physical interactions
|Contact: Leila Gray|
University of Washington