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Article: Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome
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TitleChromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome
 
AuthorsEstivill, X2 1
Cheung, J2
Pujana, MA1
Nakabayashi, K2
Scherer, SW2
Tsui, LC2
 
Issue Date2002
 
PublisherOxford University Press. The Journal's web site is located at http://hmg.oxfordjournals.org/
 
CitationHuman Molecular Genetics, 2002, v. 11 n. 17, p. 1987-1995 [How to Cite?]
DOI: http://dx.doi.org/10.1093/hmg/11.17.1987
 
AbstractWe have explored the National Center for Biotechnology Information (NCBI) single nucleotide polymorphisms (SNPs) database for a correlation between the density of putative SNPs, as well as SNPs that map to different chromosomal locations (ambiguously mapped SNPs), and segmental duplications of DNA in chromosome regions involved in genomic disorders. A high density of SNPs (14.4 and 12.4 SNPs per kb) was detected in the low copy repeats (LCRs) responsible for the chromosome 17p12 duplication and deletion that cause peripheral neuropathies. None of the SNPs at the PMP22 gene were ambiguously mapped, but 93% of the, SNPs at LCRs mapped on both LCR copies, indicating that they are in fact variants in paralogous sequences. Similarly, a high SNP density was found in the LCR regions flanking the neurofibromatosis type 1 (NF1) gene, with 80% of SNPs mapping on both LCR copies. A high density of SNPs was found within LCR sequences involved in the deletions that mediate contiguous gene syndromes on chromosomes 7q11, 15q11-q13 and 22q11. We have analyzed the whole sequence of chromosome 22, which contains 14% of ambiguously mapped SNPs, and have found a good correlation between these SNPs and segmental duplications detected by BLAST analysis. We have identified several segments of ambiguously mapped SNPs, four corresponding to LCRs involved in the chromosome 22q11 microdeletion syndromes. Our data indicate that most SNPs in LCR segments are in fact paralogous sequence variants (PSVs), and suggest that a significant proportion of the SNPs in the NCBI database correspond to PSVs within segmental duplications of the human genome sequence.
 
ISSN0964-6906
2012 Impact Factor: 7.692
2012 SCImago Journal Rankings: 4.103
 
DOIhttp://dx.doi.org/10.1093/hmg/11.17.1987
 
ISI Accession Number IDWOS:000177356600008
 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorEstivill, X
 
dc.contributor.authorCheung, J
 
dc.contributor.authorPujana, MA
 
dc.contributor.authorNakabayashi, K
 
dc.contributor.authorScherer, SW
 
dc.contributor.authorTsui, LC
 
dc.date.accessioned2007-09-12T03:52:19Z
 
dc.date.available2007-09-12T03:52:19Z
 
dc.date.issued2002
 
dc.description.abstractWe have explored the National Center for Biotechnology Information (NCBI) single nucleotide polymorphisms (SNPs) database for a correlation between the density of putative SNPs, as well as SNPs that map to different chromosomal locations (ambiguously mapped SNPs), and segmental duplications of DNA in chromosome regions involved in genomic disorders. A high density of SNPs (14.4 and 12.4 SNPs per kb) was detected in the low copy repeats (LCRs) responsible for the chromosome 17p12 duplication and deletion that cause peripheral neuropathies. None of the SNPs at the PMP22 gene were ambiguously mapped, but 93% of the, SNPs at LCRs mapped on both LCR copies, indicating that they are in fact variants in paralogous sequences. Similarly, a high SNP density was found in the LCR regions flanking the neurofibromatosis type 1 (NF1) gene, with 80% of SNPs mapping on both LCR copies. A high density of SNPs was found within LCR sequences involved in the deletions that mediate contiguous gene syndromes on chromosomes 7q11, 15q11-q13 and 22q11. We have analyzed the whole sequence of chromosome 22, which contains 14% of ambiguously mapped SNPs, and have found a good correlation between these SNPs and segmental duplications detected by BLAST analysis. We have identified several segments of ambiguously mapped SNPs, four corresponding to LCRs involved in the chromosome 22q11 microdeletion syndromes. Our data indicate that most SNPs in LCR segments are in fact paralogous sequence variants (PSVs), and suggest that a significant proportion of the SNPs in the NCBI database correspond to PSVs within segmental duplications of the human genome sequence.
 
dc.description.naturelink_to_OA_fulltext
 
dc.identifier.citationHuman Molecular Genetics, 2002, v. 11 n. 17, p. 1987-1995 [How to Cite?]
DOI: http://dx.doi.org/10.1093/hmg/11.17.1987
 
dc.identifier.doihttp://dx.doi.org/10.1093/hmg/11.17.1987
 
dc.identifier.epage1995
 
dc.identifier.isiWOS:000177356600008
 
dc.identifier.issn0964-6906
2012 Impact Factor: 7.692
2012 SCImago Journal Rankings: 4.103
 
dc.identifier.issue17
 
dc.identifier.openurl
 
dc.identifier.pmid12165560
 
dc.identifier.scopuseid_2-s2.0-0037101840
 
dc.identifier.spage1987
 
dc.identifier.urihttp://hdl.handle.net/10722/44374
 
dc.identifier.volume11
 
dc.languageeng
 
dc.publisherOxford University Press. The Journal's web site is located at http://hmg.oxfordjournals.org/
 
dc.publisher.placeUnited Kingdom
 
dc.relation.ispartofHuman Molecular Genetics
 
dc.relation.referencesReferences in Scopus
 
dc.subject.meshChromosome mapping
 
dc.subject.meshChromosomes, human, pair 22 - genetics
 
dc.subject.meshGene duplication
 
dc.subject.meshGenome, human
 
dc.subject.meshPolymorphism, single nucleotide
 
dc.titleChromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome
 
dc.typeArticle
 
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Author Affiliations
  1. Centro de Regulacion Genomica
  2. Hospital for Sick Children University of Toronto