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Assembly and analysis of 100 full MHC haplotypes from the Danish population. / Jensen, Jacob M.; Villesen, Palle; Friborg, Rune M.; Mailund, Thomas; Besenbacher, Søren; Sørensen, Lasse Maretty; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Skov, Laurits; Belling, Kirstine G; Have, Christian Theil; Izarzugaza, Jose M. G.; Grosjean, Marie; Bork-Jensen, Jette; Grove, Jakob; Als, Thomas D.; Huang, Shujia; Chang, Yuqi; Xu, Ruiqi; Ye, Weijian; Rao, Junhua; Guo, Xiaosen; Sun, Jihua; Cao, Hongzhi; Ye, Chen; Beusekom, Johan V.; Espeseth, Thomas; Flindt, Esben; Halager, Anders E.; Hellard, Stephanie Le; Hultman, Christina M.; Lescai, Francesco; Li, Shengting; Lund, Ole; Løngren, Peter; Matey-Hernandez, Maria Luisa; Mors, Ole; Pedersen, Christian N. S.; Sicheritz-Pontén, Thomas; Sullivan, Patrick; Syed, Ali; Westergaard, David; Yadav, Rachita; Li, Ning; Xu, Xun; Hansen, Torben; Bolund, Lars; Krogh, Anders; Sørensen, Thorkild I. A.; Pedersen, Oluf Borbye; Gupta, Ramneek; Rasmussen, Simon; Børglum, Anders D.; Wang, Jun; Eiberg, Hans Rudolf Lytchoff; Kristiansen, Karsten; Brunak, Søren; Schierup, Mikkel Heide.
In:
Genome Research, Vol. 27, No. 9, 09.2017, p. 1597-1607.
Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
Jensen, JM, Villesen, P, Friborg, RM, Mailund, T, Besenbacher, S, Sørensen, LM
, Petersen, B, Sibbesen, JA, Liu, S, Skov, L, Belling, KG, Have, CT, Izarzugaza, JMG, Grosjean, M, Bork-Jensen, J, Grove, J, Als, TD, Huang, S, Chang, Y, Xu, R, Ye, W, Rao, J, Guo, X, Sun, J, Cao, H, Ye, C, Beusekom, JV, Espeseth, T, Flindt, E, Halager, AE, Hellard, SL, Hultman, CM, Lescai, F, Li, S, Lund, O, Løngren, P, Matey-Hernandez, ML, Mors, O, Pedersen, CNS, Sicheritz-Pontén, T, Sullivan, P, Syed, A, Westergaard, D, Yadav, R, Li, N, Xu, X
, Hansen, T, Bolund, L
, Krogh, A, Sørensen, TIA, Pedersen, OB, Gupta, R
, Rasmussen, S, Børglum, AD, Wang, J
, Eiberg, HRL, Kristiansen, K, Brunak, S & Schierup, MH 2017, '
Assembly and analysis of 100 full MHC haplotypes from the Danish population',
Genome Research, vol. 27, no. 9, pp. 1597-1607.
https://doi.org/10.1101/gr.218891.116APA
Jensen, J. M., Villesen, P., Friborg, R. M., Mailund, T., Besenbacher, S., Sørensen, L. M.
, Petersen, B., Sibbesen, J. A., Liu, S., Skov, L., Belling, K. G., Have, C. T., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., ... Schierup, M. H. (2017).
Assembly and analysis of 100 full MHC haplotypes from the Danish population.
Genome Research,
27(9), 1597-1607.
https://doi.org/10.1101/gr.218891.116Vancouver
Jensen JM, Villesen P, Friborg RM, Mailund T, Besenbacher S, Sørensen LM et al.
Assembly and analysis of 100 full MHC haplotypes from the Danish population.
Genome Research. 2017 Sep;27(9):1597-1607.
https://doi.org/10.1101/gr.218891.116Author
Jensen, Jacob M. ; Villesen, Palle ; Friborg, Rune M. ; Mailund, Thomas ; Besenbacher, Søren ; Sørensen, Lasse Maretty ; Petersen, Bent ; Sibbesen, Jonas Andreas ; Liu, Siyang ; Skov, Laurits ; Belling, Kirstine G ; Have, Christian Theil ; Izarzugaza, Jose M. G. ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; Beusekom, Johan V. ; Espeseth, Thomas ; Flindt, Esben ; Halager, Anders E. ; Hellard, Stephanie Le ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Matey-Hernandez, Maria Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick ; Syed, Ali ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Bolund, Lars ; Krogh, Anders ; Sørensen, Thorkild I. A. ; Pedersen, Oluf Borbye ; Gupta, Ramneek ; Rasmussen, Simon ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans Rudolf Lytchoff ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide. / Assembly and analysis of 100 full MHC haplotypes from the Danish population. In: Genome Research. 2017 ; Vol. 27, No. 9. pp. 1597-1607.
Bibtex
@article{2afb6a309cd743bc93413fa686612ee7,
title = "Assembly and analysis of 100 full MHC haplotypes from the Danish population",
abstract = "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.",
author = "Jensen, {Jacob M.} and Palle Villesen and Friborg, {Rune M.} and Thomas Mailund and S{\o}ren Besenbacher and S{\o}rensen, {Lasse Maretty} and Bent Petersen and Sibbesen, {Jonas Andreas} and Siyang Liu and Laurits Skov and Belling, {Kirstine G} and Have, {Christian Theil} and Izarzugaza, {Jose M. G.} and Marie Grosjean and Jette Bork-Jensen and Jakob Grove and Als, {Thomas D.} and Shujia Huang and Yuqi Chang and Ruiqi Xu and Weijian Ye and Junhua Rao and Xiaosen Guo and Jihua Sun and Hongzhi Cao and Chen Ye and Beusekom, {Johan V.} and Thomas Espeseth and Esben Flindt and Halager, {Anders E.} and Hellard, {Stephanie Le} and Hultman, {Christina M.} and Francesco Lescai and Shengting Li and Ole Lund and Peter L{\o}ngren and Matey-Hernandez, {Maria Luisa} and Ole Mors and Pedersen, {Christian N. S.} and Thomas Sicheritz-Pont{\'e}n and Patrick Sullivan and Ali Syed and David Westergaard and Rachita Yadav and Ning Li and Xun Xu and Torben Hansen and Lars Bolund and Anders Krogh and S{\o}rensen, {Thorkild I. A.} and Pedersen, {Oluf Borbye} and Ramneek Gupta and Simon Rasmussen and B{\o}rglum, {Anders D.} and Jun Wang and Eiberg, {Hans Rudolf Lytchoff} and Karsten Kristiansen and S{\o}ren Brunak and Schierup, {Mikkel Heide}",
year = "2017",
month = sep,
doi = "10.1101/gr.218891.116",
language = "English",
volume = "27",
pages = "1597--1607",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "9",
}
RIS
TY - JOUR
T1 - Assembly and analysis of 100 full MHC haplotypes from the Danish population
AU - Jensen, Jacob M.
AU - Villesen, Palle
AU - Friborg, Rune M.
AU - Mailund, Thomas
AU - Besenbacher, Søren
AU - Sørensen, Lasse Maretty
AU - Petersen, Bent
AU - Sibbesen, Jonas Andreas
AU - Liu, Siyang
AU - Skov, Laurits
AU - Belling, Kirstine G
AU - Have, Christian Theil
AU - Izarzugaza, Jose M. G.
AU - Grosjean, Marie
AU - Bork-Jensen, Jette
AU - Grove, Jakob
AU - Als, Thomas D.
AU - Huang, Shujia
AU - Chang, Yuqi
AU - Xu, Ruiqi
AU - Ye, Weijian
AU - Rao, Junhua
AU - Guo, Xiaosen
AU - Sun, Jihua
AU - Cao, Hongzhi
AU - Ye, Chen
AU - Beusekom, Johan V.
AU - Espeseth, Thomas
AU - Flindt, Esben
AU - Halager, Anders E.
AU - Hellard, Stephanie Le
AU - Hultman, Christina M.
AU - Lescai, Francesco
AU - Li, Shengting
AU - Lund, Ole
AU - Løngren, Peter
AU - Matey-Hernandez, Maria Luisa
AU - Mors, Ole
AU - Pedersen, Christian N. S.
AU - Sicheritz-Pontén, Thomas
AU - Sullivan, Patrick
AU - Syed, Ali
AU - Westergaard, David
AU - Yadav, Rachita
AU - Li, Ning
AU - Xu, Xun
AU - Hansen, Torben
AU - Bolund, Lars
AU - Krogh, Anders
AU - Sørensen, Thorkild I. A.
AU - Pedersen, Oluf Borbye
AU - Gupta, Ramneek
AU - Rasmussen, Simon
AU - Børglum, Anders D.
AU - Wang, Jun
AU - Eiberg, Hans Rudolf Lytchoff
AU - Kristiansen, Karsten
AU - Brunak, Søren
AU - Schierup, Mikkel Heide
PY - 2017/9
Y1 - 2017/9
N2 - 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.
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.
U2 - 10.1101/gr.218891.116
DO - 10.1101/gr.218891.116
M3 - Journal article
C2 - 28774965
AN - SCOPUS:85028744509
VL - 27
SP - 1597
EP - 1607
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 9
ER -
