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Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence

Joseph Cheung1, Xavier Estivill12*, Razi Khaja1, Jeffrey R MacDonald1, Ken Lau1, Lap-Chee Tsui134 and Stephen W Scherer13*

Author Affiliations

1 Program in Genetics and Genomic Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada

2 Genes and Disease Program, Genomic Regulation Center, and Facultat Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, E-08003 Barcelona, Catalonia, Spain

3 Department of Molecular and Medical Genetics, University of Toronto, 555 University Avenue, Toronto, ON M5G 1X8, Canada

4 Current address: The University of Hong Kong, Pokfulam Road, Hong Kong

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Genome Biology 2003, 4:R25  doi:10.1186/gb-2003-4-4-r25

Published: 17 March 2003



Previous studies have suggested that recent segmental duplications, which are often involved in chromosome rearrangements underlying genomic disease, account for some 5% of the human genome. We have developed rapid computational heuristics based on BLAST analysis to detect segmental duplications, as well as regions containing potential sequence misassignments in the human genome assemblies.


Our analysis of the June 2002 public human genome assembly revealed that 107.4 of 3,043.1 megabases (Mb) (3.53%) of sequence contained segmental duplications, each with size equal or more than 5 kb and 90% identity. We have also detected that 38.9 Mb (1.28%) of sequence within this assembly is likely to be involved in sequence misassignment errors. Furthermore, we have identified a significant subset (199,965 of 2,327,473 or 8.6%) of single-nucleotide polymorphisms (SNPs) in the public databases that are not true SNPs but are potential paralogous sequence variants.


Using two distinct computational approaches, we have identified most of the sequences in the human genome that have undergone recent segmental duplications. Near-identical segmental duplications present a major challenge to the completion of the human genome sequence. Potential sequence misassignments detected in this study would require additional efforts to resolve.