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From: steven perkins <>
Subject: [DNA] Article: Characterization of X-Linked SNP genotypic variationin globally distributed human populations
Date: Sun, 21 Mar 2010 22:06:33 -0400


An interesting article on X SNPs.
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Characterization of X-Linked SNP genotypic variation in globally
distributed human populations

Full text:
http://genomebiology.com/2010/11/1/R10

Amanda M Casto1 email, Jun Z Li2 email, Devin Absher3 email, Richard
Myers3 email, Sohini Ramachandran4 email and Marcus W Feldman5 email

1 Department of Genetics, Stanford University, Mail Stop 5120,
Stanford, California 94305, USA

2 Department of Human Genetics, University of Michigan, 4909 Buhl
Building, 1241 East Catherine St, Ann Arbor, Michigan 48109, USA

3 HudsonAlpha Institute for Biotechnology, 601 Genome Way,
Huntsville, Alabama 35806, USA

4 Society of Fellows and Department of Organismic and Evolutionary
Biology, Harvard University, 26 Oxford St, Cambridge, Massachusetts
02138, USA

5 Department of Biological Sciences, Stanford University, Gilbert
Hall 108, Stanford, California 94305, USA

author email corresponding author email

Genome Biology 2010, 11:R10doi:10.1186/gb-2010-11-1-r10
Published: 28 January 2010
Abstract (provisional)

Background

The transmission pattern of the human X chromosome reduces its
population size relative to the autosomes, subjects it to
disproportionate influence by female demography, and leaves X-linked
mutations exposed to selection in males. As a result, the analysis of
X-linked genomic variation can provide insights into the influence of
demography and selection on the human genome. Here we characterize the
genomic variation represented by 16,297 X-linked SNPs genotyped in the
CEPH human genome diversity project samples.
Results

We found that X chromosomes tend to be more differentiated between
human populations than autosomes with several notable exceptions.
Comparisons between genetically distant populations also showed an
excess of X-linked SNPs with large allele frequency differences.
Combining information about these SNPs with results from tests
designed to detect selective sweeps, we identified two regions that
were clear outliers from the rest of the X chromosome for haplotype
structure and allele frequency distribution. We were also able to more
precisely define the geographical extent of some previously described
X-linked selective sweeps.
Conclusions

The relationship between male and female demographic histories is
likely to be complex as evidence supporting different conclusions can
be found in the same dataset. Although demography may have contributed
to the excess of SNPs with large allele frequency differences observed
on the X chromosome, we believe that selection is at least partially
responsible. Finally, our results reveal the geographical complexities
of selective sweeps on the X chromosome and argue for the use of
diverse populations in studies of selection.

--
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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