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Archiver > GENEALOGY-DNA > 2009-11 > 1259638713


From: steven perkins <>
Subject: [DNA] Article: SNPs for a universal individual identification panel
Date: Mon, 30 Nov 2009 22:38:33 -0500


This should be of interest in close kin analysis:
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SNPs for a universal individual identification panel

published in Human Genetics

Andrew J. Pakstis1, William C. Speed1, Rixun Fang2, Fiona C. L.
Hyland2, Manohar R. Furtado2, Judith R. Kidd1 and Kenneth K. Kidd1
Contact Information
(1) Department of Genetics, Yale University School of Medicine, 333
Cedar Street, 208005, New Haven, CT 06520, USA
(2) Applied Markets, Applied Biosystems/Life Technologies, Foster
City, CA 94404, USA

Received: 9 September 2009 Accepted: 13 November 2009 Published
online: 24 November 2009

Abstract An efficient method to uniquely identify every individual
would have value in quality control and sample tracking of large
collections of cell lines or DNA as is now often the case with whole
genome association studies. Such a method would also be useful in
forensics. SNPs represent the best markers for such purposes. We have
developed a globally applicable resource of 92 SNPs for individual
identification (IISNPs) with extremely low probabilities of any two
unrelated individuals from anywhere in the world having identical
genotypes. The SNPs were identified by screening over 500
likely/candidate SNPs on samples of 44 populations representing the
major regions of the world. All 92 IISNPs have an average
heterozygosity >0.4 and the F st values are all <0.06 on our 44
populations making these a universally applicable panel irrespective
of ethnicity or ancestry. No significant linkage disequilibrium (LD)
occurs for all unique pairings of 86 of the 92 IISNPs (median LD =
0.011) in all of the 44 populations. The remaining 6 IISNPs show
strong LD in most of the 44 populations for a small subset (7) of the
unique pairings in which they occur due to close linkage. 45 of the 86
SNPs are spread across the 22 human autosomes and show very loose or
no genetic linkage with each other. These 45 IISNPs constitute an
excellent panel for individual identification including paternity
testing with associated probabilities of individual genotypes less
than 10-15, smaller than achieved with the current panels of forensic
markers. This panel also improves on an interim panel of 40 IISNPs
previously identified using 40 population samples. The unlinked status
of the subset of 45 SNPs we have identified also makes them useful for
situations involving close biological relationships. Comparisons with
random sets of SNPs illustrate the greater discriminating power,
efficiency, and more universal applicability of this IISNP panel to
populations around the world. The full set of 86 IISNPs that do not
show LD can be used to provide even smaller genotype match
probabilities in the range of 10-31-10-35 based on the 44 population
samples studied.

Electronic supplementary material The online version of this article
(doi:10.1007/s00439-009-0771-1) contains supplementary material, which
is available to authorized users.


--
Steven C. Perkins
http://stevencperkins.com/
Online Journal of Genetics and Genealogy
http://jgg-online.blogspot.com/
Steven C. Perkins' Genealogy Page
http://stevencperkins.com/genealogy.html
Steven C. Perkins' Genealogy Blog
http://scpgen.blogspot.com/


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