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Human Molecular Genetics Advance Access published online on November 3, 2004
Human Molecular Genetics, doi:10.1093/hmg/ddi006
© 2004 by Oxford University Press
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Article

Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes

Tushar R. Bhangale 1, Mark J. Rieder 2, Robert Livingston 2, and Deborah A. Nickerson 3*

1 Departments of Bioengineering, University of Washington, Seattle, WA, USA
2 Department of Genome Sciences, University of Washington, Seattle, WA, USA
3 Departments of Bioengineering, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA, 98195-7730, USA

* To whom correspondence should be addressed.
Deborah A. Nickerson, E-mail: debnick{at}u.washington.edu


  Abstract

Despite being the second most frequent type of polymorphism in the genome, diallelic insertion-deletion polymorphisms (indels) have received far less attention in the study of sequence variation. In this report, we describe an approach that can detect indels in the heterozygous state and can comprehensively identify indels in the target sequence. Using this approach, we identified 2,393 indels in a set of 330 candidate genes i.e. an average of 7 indels per gene with about 2 indels per gene being common (minor allele frequency ≥0.1). We compared the population genetic characteristics of indels with substitutions in this data. Our data supported the findings that deletions occur more frequently in the human genome. 5'UTR and coding regions of the genes showed a significantly lower diversity for indels compared to other regions, suggesting differences in effects of selection on indels and substitutions. Sequence diversity and pairwise linkage disequilibrium (LD) findings of the different populations were similar to earlier results and included a greater skew towards low frequency variants and a faster rate of LD decay in the African-descent population compared to the non-African populations. Within populations, the allele frequency spectra and LD-decay profiles for indels were similar to substitutions. Overall, the findings suggest that, although the mechanisms giving rise to indels may be different from those causing substitutions, the evolutionary histories of indels and substitutions are similar, and that indels can play a valuable role in association studies and in marker selection strategies.


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