8c2f7318d8d821de9b2a25750586a94ab5e8c1bb
lrnassar
  Fri Nov 15 18:50:19 2024 -0800
Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM.

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 <H2>Description</H2>
 <P>
 This track shows a 3-SNP moving average of 
 <em>p(1-p)</em> where <em>p</em> is the major allele frequency
 (i.e. half of the expected heterozygosity) 
 on seven continents,
 from SNPs genotyped in 53 populations worldwide by the 
-<A HREF="http://www.stanford.edu/group/morrinst/hgdp.html" TARGET=_BLANK>Human 
+<A HREF="https://web.stanford.edu/group/morrinst/hgdp.html" TARGET=_BLANK>Human 
 Genome Diversity Project</A> in collaboration with the
 <A HREF="https://cephb.fr/en/cephdb/" TARGET=_BLANK>Centre d'Etude 
 du Polymorphisme Humain</A> (HGDP-CEPH).
 This track and several others are available from the 
 <A HREF="http://hgdp.uchicago.edu/" TARGET=_BLANK>HGDP Selection Browser</A>.
 </P>
 
 <H2>Methods</H2>
 <P>
 Samples collected by the HGDP-CEPH from 1,043 individuals from around the
 world were genotyped for 657,000 SNPs at
 <A HREF="https://hagsc.org/hgdp/" TARGET=_BLANK>Stanford</A>.
 The 53 populations were divided into seven continental groups: Africa,
 Middle East, Europe, South Asia, East Asia, Oceania and the Americas.
 Allele frequencies were used to calculate <em>p(1-p)</em> 
 for each SNP, and then a
 3-SNP average was computed for each SNP and its two neighboring SNPs.</P>
 
 <P>
 The associated analysis tracks HGDP FST, HGP iHS, and HGDP XP-EHH
 (Pickrell <em>et al.</em>) did not make use of all African populations, but
 instead used only the Bantu populations because a more closely related
 group was desired for comparison with other continental groups.
 For this track, separate subtracks show the expected heterozygosity 
 of all African populations and of only Bantu populations.
 </P>
 
 <H2>Credits</H2>
 <P>
 Thanks to the HGDP-CEPH and Joe Pickrell in the 
 <A HREF="http://web.stanford.edu/group/pritchardlab/home.html"TARGET=_BLANK>Pritchard
 lab</A> at the University of Chicago for providing these data.
 </P>
 
 
 <H2>References</H2>
 <P>
 Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li J, Absher D,
 Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK.
 <A HREF="https://www.ncbi.nlm.nih.gov/pubmed/19307593?dopt=Abstract"
 TARGET=_BLANK>Signals of recent positive selection in a worldwide sample of
 human populations</A>. <em>Genome Res.</em> 2009 May;19(5):826-37.</P>
 
 <P>
 Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S,
 Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM.
 <A HREF="https://www.ncbi.nlm.nih.gov/pubmed/18292342?dopt=Abstract"
 TARGET=_BLANK>Worldwide human relationships inferred from genome-wide
 patterns of variation</A>. <em>Science</em>. 2008 Feb 22;319(5866):1100-4.</P>
 
 <P>
 Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer
 J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A <em>et al.</em>
 <A HREF="https://www.ncbi.nlm.nih.gov/pubmed/11954565?dopt=Abstract" 
 TARGET=_BLANK>A human genome diversity cell line panel</A>.
 <em>Science</em>. 2002 Apr 12;296(5566):261-2.</P>