Refining the genome

A comparison of human genome sequences produced using different approaches by the International Human Genome Sequencing Consortium and the private firm Celera reveals that whole genome shotgun sequencing (WGS), as used by Celera, fails miserably on genome segmental duplications.

Writing in Nature this week, Evan Eichler, from Washington University, and colleagues show that WGS does very well for 95% of euchromatin, but falls down in the very large duplications that are greater than 98% identical and longer than 20 kb in size. "It's not that bad unless you really care about those large identical duplications," he told The Scientist. The technique "fails and fails miserably" in that regard, he said.

For the current study, Eichler teamed up with previous collaborators Granger G. Sutton and Aaron L. Halpern, both now at the J. Craig Venter Institute in Rockville, Md., in an apparent revisiting of results published by PNAS...