RT Journal
A1 Jensen, Jacob M.
A1 Villesen, Palle
A1 Friborg, Rune M.
A1 The Danish Pan-Genome Consortium
A1 Mailund, Thomas
A1 Besenbacher, Søren
A1 Schierup, Mikkel H.
T1 Assembly and analysis of 100 full MHC haplotypes from the Danish population
JF Genome Research 
JO Genome Research 
YR 2017 
FD September 01 
VO 27 
IS 9 
SP 1597 
OP 1607 
DO 10.1101/gr.218891.116 
UL http://genome.cshlp.org/content/27/9/1597.abstract 
AB Genes in the major histocompatibility complex (MHC, also known as HLA) play a critical role in the immune response and variation within the extended 4-Mb region shows association with major risks of many diseases. Yet, deciphering the underlying causes of these associations is difficult because the MHC is the most polymorphic region of the genome with a complex linkage disequilibrium structure. Here, we reconstruct full MHC haplotypes from de novo assembled trios without relying on a reference genome and perform evolutionary analyses. We report 100 full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data. We also present the first complete analysis of the recombination landscape in the entire region and show how balancing selection at classical genes have linked effects on the frequency of variants throughout the region.