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

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Dokumenter

  • Jacob M. Jensen
  • Palle Villesen
  • Rune M. Friborg
  • Thomas Mailund
  • Søren Besenbacher
  • Lasse Maretty Sørensen
  • Jonas Andreas Sibbesen
  • Siyang Liu
  • Laurits Skov
  • Christian Theil Have
  • Jose M. G. Izarzugaza
  • Marie Grosjean
  • Jette Bork-Jensen
  • Jakob Grove
  • Thomas D. Als
  • Shujia Huang
  • Yuqi Chang
  • Ruiqi Xu
  • Weijian Ye
  • Junhua Rao
  • Xiaosen Guo
  • 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
  • Lars Bolund
  • Ramneek Gupta
  • Anders D. Børglum
  • Jun Wang
  • 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.

OriginalsprogEngelsk
TidsskriftGenome Research
Vol/bind27
Udgave nummer9
Sider (fra-til)1597-1607
Antal sider11
ISSN1088-9051
DOI
StatusUdgivet - sep. 2017

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