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Letter
Nature Genetics 38, 82 - 85 (2006)
Published online: 4 December 2005; | doi:10.1038/ng1695

Common deletions and SNPs are in linkage disequilibrium in the human genome

David A Hinds1, 2, Andrew P Kloek1, 2, Michael Jen1, Xiyin Chen1 & Kelly A Frazer1

1  Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, California 94043, USA.

2  These authors contributed equally to this work.

Correspondence should be addressed to Kelly A Frazer kelly_frazer@perlegen.com

Humans show great variation in phenotypic traits such as height, eye color and susceptibility to disease. Genomic DNA sequence differences among individuals are responsible for the inherited components of these complex traits. Reports suggest that intermediate and large-scale DNA copy number and structural variations are prevalent enough to be an important source of genetic variation between individuals1, 2, 3, 4, 5, 6, 7, 8. Because association studies to identify genomic loci associated with particular phenotypic traits have focused primarily on genotyping SNPs, it is important to determine whether common structural polymorphisms are in linkage disequilibrium with common SNPs, and thus can be assessed indirectly in SNP-based studies. Here we examine 100 deletion polymorphisms ranging from 70 bp to 7 kb. We show that common deletions and SNPs ascertained with similar criteria have essentially the same distribution of linkage disequilibrium with surrounding SNPs, indicating that these polymorphisms may share evolutionary history and that most deletion polymorphisms are effectively assayed by proxy in SNP-based association studies.


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