Assembly and analysis of 100 full MHC haplotypes from the Danish population

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Jacob M. Jensen, Palle Villesen, Rune M. Friborg, Thomas Mailund, Søren Besenbacher, Lasse Maretty Sørensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Laurits Skov, Kirstine G Belling, Christian Theil Have, Jose M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu & 39 others Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun, Hongzhi Cao, Chen Ye, Johan V. Beusekom, Thomas Espeseth, Esben Flindt, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngren, Maria Luisa Matey-Hernandez, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Lars Bolund, Anders Krogh, Thorkild I. A. Sørensen, Oluf Borbye Pedersen, Ramneek Gupta, Simon Rasmussen, Anders D. Børglum, Jun Wang, Hans Rudolf Lytchoff Eiberg, Karsten Kristiansen, Søren Brunak, Mikkel Heide Schierup

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.

Original languageEnglish
JournalGenome Research
Issue number9
Pages (from-to)1597-1607
Number of pages11
Publication statusPublished - Sep 2017

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