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Closing gaps in the human genome using sequencing by synthesis

Manuel Garber1, Michael C Zody12, Harindra M Arachchi1, Aaron Berlin1, Sante Gnerre1, Lisa M Green1, Niall Lennon1 and Chad Nusbaum1*

Author Affiliations

1 Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA

2 Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 24 Uppsala, Sweden

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Genome Biology 2009, 10:R60  doi:10.1186/gb-2009-10-6-r60

Published: 2 June 2009

Abstract

The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural' in nature. Another class of gaps is likely to be refractory to clone-based approaches, and cannot be approached in ways previously described. We present an approach for closing these gaps using 454 sequencing. As a proof of principle, we closed all three remaining non-structural gaps in chromosome 15.