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

TitleGenome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.
Authors
Issue Date2003
PublisherBioMed Central Ltd.
Citation
Genome Biology, 2003, v. 4 n. 4, p. R25 How to Cite?
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.
Persistent Identifierhttp://hdl.handle.net/10722/43556
ISSN
PubMed Central ID
ISI Accession Number ID

 

Author Affiliations
  1. Hospital for Sick Children University of Toronto
DC FieldValueLanguage
dc.contributor.authorCheung, Jen_HK
dc.contributor.authorEstivill, Xen_HK
dc.contributor.authorKhaja, Ren_HK
dc.contributor.authorMacDonald, JRen_HK
dc.contributor.authorLau, Ken_HK
dc.contributor.authorTsui, LCen_HK
dc.contributor.authorScherer, SWen_HK
dc.date.accessioned2007-03-23T04:48:55Z-
dc.date.available2007-03-23T04:48:55Z-
dc.date.issued2003en_HK
dc.identifier.citationGenome Biology, 2003, v. 4 n. 4, p. R25en_HK
dc.identifier.issn1465-6914en_HK
dc.identifier.urihttp://hdl.handle.net/10722/43556-
dc.description.abstractBACKGROUND: 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.en_HK
dc.format.extent856152 bytes-
dc.format.extent25088 bytes-
dc.format.mimetypeapplication/pdf-
dc.format.mimetypeapplication/msword-
dc.languageengen_HK
dc.publisherBioMed Central Ltd.en_HK
dc.relation.ispartofGenome biologyen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshArtifactsen_HK
dc.subject.meshChromosomes, humanen_HK
dc.subject.meshComputational biologyen_HK
dc.subject.meshGene duplicationen_HK
dc.subject.meshGenetic diseases, inborn - geneticsen_HK
dc.titleGenome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.en_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1465-6906&volume=4&issue=4&spage=R25:1&epage=10&date=2003&atitle=Genome-wide+detection+of+segmental+duplications+and+potential+assembly+errors+in+the+human+genome+sequenceen_HK
dc.identifier.emailTsui, LC: tsuilc@hkucc.hku.hken_HK
dc.identifier.authorityTsui, LC=rp00058en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1186/gb-2003-4-4-r25en_HK
dc.identifier.pmid12702206en_HK
dc.identifier.pmcidPMC154576-
dc.identifier.scopuseid_2-s2.0-0037837485en_HK
dc.identifier.volume4en_HK
dc.identifier.issue4en_HK
dc.identifier.spageR25en_HK
dc.identifier.epageR25en_HK
dc.identifier.isiWOS:000182696200007-
dc.identifier.scopusauthoridCheung, J=7202072292en_HK
dc.identifier.scopusauthoridEstivill, X=36047834200en_HK
dc.identifier.scopusauthoridKhaja, R=7801610375en_HK
dc.identifier.scopusauthoridMacDonald, JR=7401439417en_HK
dc.identifier.scopusauthoridLau, K=36722697000en_HK
dc.identifier.scopusauthoridTsui, LC=7102754167en_HK
dc.identifier.scopusauthoridScherer, SW=35374654500en_HK
dc.identifier.citeulike838938-

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