Regions of high linkage disequilibrium (LD)

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There are regions of long-range, high linkage diequilibrium in the human genome [1][2]. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

Here is a lost of positions for GRCH Build 37 <tab border="1" head="top"> Chr Start Stop ID 1 48000000 52000000 2 86000000 100500000 2 134500000 138000000 2 183000000 190000000 3 47500000 50000000 3 83500000 87000000 3 89000000 97500000 5 44500000 50500000 5 98000000 100500000 5 129000000 132000000 5 135500000 138500000 6 25000000 35000000 6 57000000 64000000 6 140000000 142500000 7 55000000 66000000 8 7000000 13000000 8 43000000 50000000 8 112000000 115000000 10 37000000 43000000 11 46000000 57000000 11 87500000 90500000 12 33000000 40000000 12 109500000 112000000 20 32000000 34500000 </tab>


These positions are for GRCH build 36. <tab border="1" head="top"> Chr Start Stop ID 1 48060567 52060567 hild1 2 85941853 100407914 hild2 2 134382738 137882738 hild3 2 182882739 189882739 hild4 3 47500000 50000000 hild5 3 83500000 87000000 hild6 3 89000000 97500000 hild7 5 44500000 50500000 hild8 5 98000000 100500000 hild9 5 129000000 132000000 hild10 5 135500000 138500000 hild11 6 25500000 33500000 hild12 6 57000000 64000000 hild13 6 140000000 142500000 hild14 7 55193285 66193285 hild15 8 8000000 12000000 hild16 8 43000000 50000000 hild17 8 112000000 115000000 hild18 10 37000000 43000000 hild19 11 46000000 57000000 hild20 11 87500000 90500000 hild21 12 33000000 40000000 hild22 12 109521663 112021663 hild23 20 32000000 34500000 hild24 X 14150264 16650264 hild25 X 25650264 28650264 hild26 X 33150264 35650264 hild27 X 55133704 60500000 hild28 X 65133704 67633704 hild29 X 71633704 77580511 hild30 X 80080511 86080511 hild31 X 100580511 103080511 hild32 X 125602146 128102146 hild33 X 129102146 131602146 hild34 </tab>

Excluding Regions With Plink

You can remove these regions from a PED file using the following PLINK commands. Assuming you have the data stored in a file named "high-ld.txt" 

   plink --file mydata --make-set high-ld.txt --write-set --out hild
  plink --file mydata --exclude hild.set --recode --out mydatatrimmed

References

  1. ↑ Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147
  2. ↑ Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010
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