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Letter
Nature Genetics 38, 75 - 81 (2006)
Published online: 4 December 2005; | doi:10.1038/ng1697

A high-resolution survey of deletion polymorphism in the human genome

Donald F Conrad1, T Daniel Andrews2, Nigel P Carter2, Matthew E Hurles2 & Jonathan K Pritchard1

1  Department of Human Genetics, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.

2  Genome Dynamics and Evolution Group, The Wellcome Trust, Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

Correspondence should be addressed to Jonathan K Pritchard pritch@uchicago.edu

Recent work has shown that copy number polymorphism is an important class of genetic variation in human genomes1, 2, 3, 4. Here we report a new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions. We applied this method to data from the International HapMap Project5 to produce the first high-resolution population surveys of deletion polymorphism. Approximately 100 of these deletions have been experimentally validated using comparative genome hybridization on tiling-resolution oligonucleotide microarrays. Our analysis identifies a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the families. Notably, we estimate that typical individuals are hemizygous for roughly 30–50 deletions larger than 5 kb, totaling around 550–750 kb of euchromatic sequence across their genomes. The detected deletions span a total of 267 known and predicted genes. Overall, however, the deleted regions are relatively gene-poor, consistent with the action of purifying selection against deletions. Deletion polymorphisms may well have an important role in the genetics of complex traits; however, they are not directly observed in most current gene mapping studies. Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data.


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Nature Genetics
ISSN: 1061-4036
EISSN: 1546-1718
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