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

Abstract

Background 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. Results 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. Conclusion 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.

Cited by papers we hold 10

• Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus. · 2014
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• Genome assembly forensics: finding the elusive mis-assembly · 2008
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• Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies · 2007
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• Evolutionary implications of inversions that have caused intra-strand parity in DNA · 2007
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• A High-Resolution Map of Segmental DNA Copy Number Variation in the Mouse Genome · 2007
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• The Diploid Genome Sequence of an Individual Human · 2007
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• Duplication and relocation of the functional <it>DPY19L2 </it>gene within low copy repeats · 2006
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• Discovery of Human Inversion Polymorphisms by Comparative Analysis of Human and Chimpanzee DNA Sequence Assemblies · 2005
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• Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution · 2004
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• Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers · 2004
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