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Human Molecular Genetics Advance Access originally published online on September 14, 2004
Human Molecular Genetics 2004 13(21):2557-2565; doi:10.1093/hmg/ddh294
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Human Molecular Genetics, Vol. 13, No. 21 © Oxford University Press 2004; all rights reserved

Efficiency and consistency of haplotype tagging of dense SNP maps in multiple samples

Xiayi Ke1, Caroline Durrant1, Andrew P. Morris1, Sarah Hunt2, David R. Bentley2, Panos Deloukas2 and Lon R. Cardon1,*

1Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK and 2Wellcome Trust Sanger Institute, Hinxton, UK

Received June 18, 2004; Revised August 17, 2004; Accepted September 8, 2004

Haplotype tagging is a means of retaining most of the information in high density marker maps, while reducing genotyping requirements. Estimates of the numbers of tagging SNPs required to cover the human genome have varied widely, ranging from 100 000 to 1 000 000. Tagging has been applied to a number of gene-based datasets but has not been evaluated in contexts reflecting those of genome-wide association studies—large chromosome regions and multiple samples drawn from the same population. We analysed 5000 common markers across a 10 Mb segment of human chromosome 20 in three samples (UK Caucasian, CEPH Caucasian, African American) to evaluate tagging efficiency and consistency. Overall, the results indicate a high degree of efficiency, yielding 3–5-fold savings in Caucasians and 2–3-fold savings in African Americans. These levels varied according to linkage disequilibrium (LD) levels, tagging thresholds and allele frequencies, but in high LD regions they did not vary markedly due to marker density. However, a strong positive relationship between marker density and tagging was observed, relating to the fact that increasing marker density yields greater sequence coverage in high LD, thus requiring more tag SNPs to cover a greater fraction of the genome. Encouragingly, whatever the density employed, a high level of robustness was observed between UK and CEPH samples, as most of the htSNPs selected in one sample were also appropriate as tags in the other.

* To whom correspondence should be addressed at: Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Tel: +44 1865287591; Fax: +44 1865287697; Email: lon{at}well.ox.ac.uk


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