Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

The Effect of SNP Marker Density on the Efficacy of Haplotype Tagging SNPs – a Warning

The Effect of SNP Marker Density on the Efficacy of Haplotype Tagging SNPs – a Warning We investigate here the efficacy of selecting haplotype tagging SNPs at different marker densities (2kb‐10kb). Our results are based on publicly available data on 5324 markers with a median spacing of 1kb from chromosome 20. We find that whatever density of SNPs is used, htSNP analysis indicates in most cases that at least 80% of the variation can be captured using a subset of SNPs. However, as marker density decreases these htSNPs become increasingly unreliable. In this dataset htSNPs were selected to capture at least 80% of the variation at every observed SNP. At an observed SNP density of 2kb, htSNP analysis suggests that the htSNPs capture on average 95% of the observed variation, when in fact they capture 88% of the unobserved variation. At a density of 10kb, htSNP analysis suggests that 93% of the observed variation was captured, when in fact they capture on average only 78%. Our results indicate that htSNP analysis is only reliable when markers are dense – a spacing of even 2kb shows a considerable loss of information. Such findings are important both for individual studies utilising htSNPs to reduce costs, and for projects such as HapMap which try to characterise human genomic variation using htSNPs. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Annals of Human Genetics Wiley

The Effect of SNP Marker Density on the Efficacy of Haplotype Tagging SNPs – a Warning

Iles, Mark M.
Annals of Human Genetics , Volume 69 (2) – Mar 1, 2005
Download PDF
7 pages

Loading next page...
 
/lp/wiley/the-effect-of-snp-marker-density-on-the-efficacy-of-haplotype-tagging-B40kGFZXvC

References (17)

Publisher
Wiley
Copyright
Copyright © 2005 Wiley Subscription Services, Inc., A Wiley Company
ISSN
0003-4800
eISSN
1469-1809
DOI
10.1046/j.1469-1809.2004.00141.x
Publisher site
See Article on Publisher Site

Abstract

We investigate here the efficacy of selecting haplotype tagging SNPs at different marker densities (2kb‐10kb). Our results are based on publicly available data on 5324 markers with a median spacing of 1kb from chromosome 20. We find that whatever density of SNPs is used, htSNP analysis indicates in most cases that at least 80% of the variation can be captured using a subset of SNPs. However, as marker density decreases these htSNPs become increasingly unreliable. In this dataset htSNPs were selected to capture at least 80% of the variation at every observed SNP. At an observed SNP density of 2kb, htSNP analysis suggests that the htSNPs capture on average 95% of the observed variation, when in fact they capture 88% of the unobserved variation. At a density of 10kb, htSNP analysis suggests that 93% of the observed variation was captured, when in fact they capture on average only 78%. Our results indicate that htSNP analysis is only reliable when markers are dense – a spacing of even 2kb shows a considerable loss of information. Such findings are important both for individual studies utilising htSNPs to reduce costs, and for projects such as HapMap which try to characterise human genomic variation using htSNPs.

Journal

Annals of Human Genetics – Wiley

Published: Mar 1, 2005

There are no references for this article.