Article open access publication

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

Genome Research, Cold Spring Harbor Laboratory, ISSN 1088-9051

Volume 27, 9, 2017

DOI:10.1101/gr.218891.116, Dimensions: pub.1090995815, PMC: PMC5580718, PMID: 28774965,



  1. (1) Aarhus University, grid.7048.b, AU
  2. (2) Aarhus University Hospital, grid.154185.c, Central Denmark Region
  3. (3) University of Copenhagen, grid.5254.6, KU
  4. (4) Technical University of Denmark, grid.5170.3, DTU
  5. (5) BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen N, Denmark
  6. (6) Lundbeck Foundation, grid.452548.a
  7. (7) South China University of Technology, grid.79703.3a
  8. (8) Beijing Genomics Institute, grid.21155.32
  9. (9) University of Oslo, grid.5510.1
  10. (10) University of Bergen, grid.7914.b
  11. (11) Haukeland University Hospital, grid.412008.f
  12. (12) Karolinska Institute, grid.4714.6
  13. (13) University of North Carolina at Chapel Hill, grid.10698.36
  14. (14) Bispebjerg Hospital, grid.411702.1, Capital Region


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.


Research Categories

Main Subject Area

Fields of Research

Links & Metrics

NORA University Profiles

Aarhus University

University of Copenhagen

Technical University of Denmark

Dimensions Citation Indicators

Times Cited: 8

Field Citation Ratio (FCR): 1.69

Relative Citation ratio (RCR): 0.55

Open Access Info