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<title>Tagger: A haplotype map of the extended human MHC</title>

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<h1 class="science">A haplotype map of the extended human MHC</h1>


<p>Identification of susceptibility loci in infectious and autoimmune diseases is challenging due to linkage disequilibrium that extends across the major histocompatibility complex in the human genome. 
The extended MHC is a region of around 8-Mb on chromosome 6 containing over 250 protein-coding genes. 
Recently, an international consortium of researchers created a resource to characterize the LD patterns between the highly polymorphic HLA genes and background variation by typing the classical HLA genes and &gt;7,500 common SNPs and deletion-insertion polymorphisms across four population samples. </p>


<h2>Download</h2>

<ul>
<li>Phased haplotypes: <a href="download/mhc_yri.phased">YRI</a> | <a href="download/mhc_ceu.phased">CEU+</a> | <a href="download/mhc_hcb.phased">CHB</a> | <a href="download/mhc_jpt.phased">JPT</a> (PHASE format, original files from Jonathan Marchini)</li>
<li>Marker information: <a href="download/mhc_yri.sites">YRI</a> | <a href="download/mhc_ceu.sites">CEU+</a> | <a href="download/mhc_hcb.sites">CHB</a> | <a href="download/mhc_jpt.sites">JPT</a> (original files from Jonathan Marchini)<br>All positions are relative to NCBI build 34.</li>
<li>Phased haplotypes: <a href="download/mhc_yri.emppp">YRI</a> | <a href="download/mhc_ceu.emppp">CEU+</a> | <a href="download/mhc_hcb.emppp">CHB</a> | <a href="download/mhc_jpt.emppp">JPT</a><br>These files are in Nick Patterson format. Alleles for the SNPs are coded as 1=A, 2=C, 3=G, 4=T.  HLA alleles are down-coded as multiple binary alleles where 0=absent, 1=present.   </li>
<li>Marker information: <a href="download/mhc_yri.info">YRI</a> | <a href="download/mhc_ceu.info">CEU+</a> | <a href="download/mhc_hcb.info">CHB</a> | <a href="download/mhc_jpt.info">JPT</a><br>All positions are relative to NCBI build 34.</li>
<li>Phased haplotypes: <a href="download/mhc_yri.for_marcos">YRI</a> | <a href="download/mhc_ceu.for_marcos">CEU+</a> | <a href="download/mhc_hcb.for_marcos">CHB</a> | <a href="download/mhc_jpt.for_marcos">JPT</a> (no allele down-coding, and with CEPH sample IDs)</li>
<li>List of tags for HLA alleles: <a href="download/SupplTable3_062006R.xls.pdf">Supplementary Table 3</a> from de Bakker <i>et al</i>.</li>
</ul>

<h2>Links</h2>
<ul>
<li><a href="http://www.inflammgen.org">Laboratory in Genetics and Genomics Medicine of Inflammation, Montreal Heart Institute</a>
<li><a href="http://www.sanger.ac.uk/HGP/Chr6/">Wellcome Trust Sanger Institute</a> (human chromosome 6 project)</li>
</ul>

<h2>Reference</h2>

<p>P.I.W. de Bakker, G. McVean, P.C. Sabeti, M.M. Miretti, T. Green, J. Marchini, X. Ke, A.J. Monsuur, P. Whittaker, M. Delgado, J. Morrison, A. Richardson, E.C. Walsh, X. Gao, L. Galver, J. Hart, D.A. Hafler, M. Pericak-Vance, J.A. Todd, M.J. Daly, J. Trowsdale, C. Wijmenga, T.J. Vyse, S. Beck, S.S. Murray, M. Carrington, S. Gregory, P. Deloukas, J.D. Rioux (2006) <a href="http://www.nature.com/ng/journal/v38/n10/abs/ng1885.html">A high resolution HLA and SNP haplotype map for disease association studies in the extended human MHC</a>. <i>Nature Genetics</i>. <b>38</b>: 1166-1172</p>

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