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- Title
A high-resolution survey of deletion polymorphism in the human genome.
- Authors
Conrad, Donald F.; Andrews, T. Daniel; Carter, Nigel P.; Hurles, Matthew E.; Pritchard, Jonathan K.
- Abstract
Recent work has shown that copy number polymorphism is an important class of genetic variation in human genomes. 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 Project 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.
- Subjects
HUMAN genome; GENETIC polymorphisms; COMPARATIVE genomic hybridization; OLIGONUCLEOTIDES; PROTEIN microarrays; CHROMOSOMES
- Publication
Nature Genetics, 2006, Vol 38, Issue 1, p75
- ISSN
1061-4036
- Publication type
Article
- DOI
10.1038/ng1697