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, X1 2
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
2011 Impact Factor: 7.636
2011 SCImago Journal Rankings: 1.308
DOIhttp://dx.doi.org/10.1093/hmg/11.17.1987
ISI Accession Number IDWOS:000177356600008
ReferencesReferences in Scopus
DC Field
Value
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
2011 Impact Factor: 7.636
2011 SCImago Journal Rankings: 1.308
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
Author Affiliations
  1. Centro de Regulacion Genomica
  2. Hospital for Sick Children, Toronto