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Open Access Highly Accessed Research

A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population

Valeria Mattiangeli12, Anthony W Ryan23, Ross McManus23 and Daniel G Bradley1*

Author Affiliations

1 Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland

2 Department of Clinical Medicine, Trinity Centre for Health Science; Institute of Molecular Medicine, Dublin Molecular Medicine Centre, St James's Hospital, Dublin, Ireland

3 Trinity College, Dublin, Ireland

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Genome Biology 2006, 7:R74  doi:10.1186/gb-2006-7-8-r74

Published: 11 August 2006

Abstract

Background

In this study we present a single population test (Ewens-Waterson) applied in a genomic context to investigate the presence of recent positive selection in the Irish population. The Irish population is an interesting focus for the investigation of recent selection since several lines of evidence suggest that it may have a relatively undisturbed genetic heritage.

Results

We first identified outlier single nucleotide polymorphisms (SNPs), from previously published genome-wide data, with high FST branch specification in a European-American population. Eight of these were chosen for further analysis. Evidence for selective history was assessed using the Ewens-Watterson's statistic calculated using Irish genotypes of microsatellites flanking the eight outlier SNPs. Evidence suggestive of selection was detected in three of these by comparison with a population-specific genome-wide empirical distribution of the Ewens-Watterson's statistic.

Conclusion

The cystic fibrosis gene, a disease that has a world maximum frequency in Ireland, was among the genes showing evidence of selection. In addition to the demonstrated utility in detecting a signature of natural selection, this approach has the particular advantage of speed. It also illustrates concordance between results drawn from alternative methods implemented in different populations.