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


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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Figure 1: Identification and validation of deletion polymorphisms.
Figure 2: Minor allele frequencies of deletion polymorphisms and SNPs selected with similar ascertainment criteria in the Discovery Panel.
Figure 3: Linkage disequilibrium between common deletions and SNPs.


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We thank D. Cox for discussions and comments on the manuscript.

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Correspondence to Kelly A Frazer.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Deletion chromosomal positions, frequencies and PCR primer sequnces. (XLS 43 kb)

Supplementary Table 2

Deletion genotypes for individuals in the Discovery Panel. (XLS 53 kb)

Supplementary Table 3

Deletion genotype for African American individuals in the Diversity Panel. (XLS 130 kb)

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Hinds, D., Kloek, A., Jen, M. et al. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 38, 82–85 (2006).

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