Regions of high linkage disequilibrium (LD)

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

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 23 14150264 16650264 hild25 23 25650264 28650264 hild26 23 33150264 35650264 hild27 23 55133704 60500000 hild28 23 65133704 67633704 hild29 23 71633704 77580511 hild30 23 80080511 86080511 hild31 23 100580511 103080511 hild32 23 125602146 128102146 hild33 23 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