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Human Molecular Genetics, 2002, Vol. 11, No. 17 1987-1995
© 2002 Oxford University Press

Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome

Xavier Estivill1,2,*, Joseph Cheung1, Miguel Angel Pujana2, Kazuhiko Nakabayashi1, Stephen W. Scherer1 and Lap-Chee Tsui1

1Program in Genetics & Genomic Biology, Research Institute, The Hospital for Sick Children, and Department of Molecular and Medical Genetics, University of Toronto, Toronto M5G 1X8, Canada; and 2Genes & Disease Program, Genomic Regulation Center, Passeig Marítim 37–49, 08003 Barcelona, Catalonia, Spain

Received April 5, 2002; Accepted June 17, 2002

We 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.

* To whom correspondence should be addressed at: Program in Genetics and Genomic Biology, Research Institute, The Hospital for Sick Children, Room 9107C, Elm Wing Annex, The Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8 Canada. Tel: +416 8132152; Fax: +416 8138319; Email: estivill{at}genet.sickkids.on.ca; xavier.estivill{at}crg.es


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