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Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

Publikation: Bidrag til tidsskriftLetterForskningfagfællebedømt

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Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. / Sørensen, Lasse Maretty; Jensen, Jacob Malte; Petersen, Bent; Sibbesen, Jonas Andreas; Liu, Siyang; Villesen, Palle; 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; van Beusekom, Johan; Espeseth, Thomas; Flindt, Esben; Friborg, Rune M.; Halager, Anders E.; Le Hellard, Stephanie; Hultman, Christina M.; Lescai, Francesco; Li, Shengting; Lund, Ole; Løngren, Peter; Mailund, Thomas; 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; Krogh, Anders; Bolund, Lars; Sørensen, Thorkild I. A.; Pedersen, Oluf Borbye; Gupta, Ramneek; Rasmussen, Simon; Besenbacher, Søren; Børglum, Anders D.; Wang, Jun; Eiberg, Hans Rudolf Lytchoff; Kristiansen, Karsten; Brunak, Søren; Schierup, Mikkel Heide.

I: Nature, Bind 548, Nr. 7665, 2017, s. 87-91.

Publikation: Bidrag til tidsskriftLetterForskningfagfællebedømt

Harvard

Sørensen, LM, Jensen, JM, Petersen, B, Sibbesen, JA, Liu, S, Villesen, P, 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, van Beusekom, J, Espeseth, T, Flindt, E, Friborg, RM, Halager, AE, Le Hellard, S, Hultman, CM, Lescai, F, Li, S, Lund, O, Løngren, P, Mailund, T, Matey-Hernandez, ML, Mors, O, Pedersen, CNS, Sicheritz-Pontén, T, Sullivan, P, Syed, A, Westergaard, D, Yadav, R, Li, N, Xu, X, Hansen, T, Krogh, A, Bolund, L, Sørensen, TIA, Pedersen, OB, Gupta, R, Rasmussen, S, Besenbacher, S, Børglum, AD, Wang, J, Eiberg, HRL, Kristiansen, K, Brunak, S & Schierup, MH 2017, 'Sequencing and de novo assembly of 150 genomes from Denmark as a population reference', Nature, bind 548, nr. 7665, s. 87-91. https://doi.org/10.1038/nature23264

APA

Sørensen, L. M., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S., Villesen, P., ... Schierup, M. H. (2017). Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature, 548(7665), 87-91. https://doi.org/10.1038/nature23264

Vancouver

Sørensen LM, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P o.a. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature. 2017;548(7665):87-91. https://doi.org/10.1038/nature23264

Author

Sørensen, Lasse Maretty ; Jensen, Jacob Malte ; Petersen, Bent ; Sibbesen, Jonas Andreas ; Liu, Siyang ; Villesen, Palle ; 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 ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders E. ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; 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 ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf Borbye ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans Rudolf Lytchoff ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide. / Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. I: Nature. 2017 ; Bind 548, Nr. 7665. s. 87-91.

Bibtex

@article{44a5fc36f8c34b82a8f3989d54e4b510,
title = "Sequencing and de novo assembly of 150 genomes from Denmark as a population reference",
abstract = "Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits1, 2, 3, 4. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly2, 5, 6, 7. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology4, 8, 9, 10, 11, 12, 13. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.",
author = "S{\o}rensen, {Lasse Maretty} and Jensen, {Jacob Malte} and Bent Petersen and Sibbesen, {Jonas Andreas} and Siyang Liu and Palle Villesen 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 {van Beusekom}, Johan and Thomas Espeseth and Esben Flindt and Friborg, {Rune M.} and Halager, {Anders E.} and {Le Hellard}, Stephanie and Hultman, {Christina M.} and Francesco Lescai and Shengting Li and Ole Lund and Peter L{\o}ngren and Thomas Mailund 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 Anders Krogh and Lars Bolund and S{\o}rensen, {Thorkild I. A.} and Pedersen, {Oluf Borbye} and Ramneek Gupta and Simon Rasmussen and S{\o}ren Besenbacher 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",
doi = "10.1038/nature23264",
language = "English",
volume = "548",
pages = "87--91",
journal = "Nature",
issn = "0028-0836",
publisher = "nature publishing group",
number = "7665",

}

RIS

TY - JOUR

T1 - Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

AU - Sørensen, Lasse Maretty

AU - Jensen, Jacob Malte

AU - Petersen, Bent

AU - Sibbesen, Jonas Andreas

AU - Liu, Siyang

AU - Villesen, Palle

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 - van Beusekom, Johan

AU - Espeseth, Thomas

AU - Flindt, Esben

AU - Friborg, Rune M.

AU - Halager, Anders E.

AU - Le Hellard, Stephanie

AU - Hultman, Christina M.

AU - Lescai, Francesco

AU - Li, Shengting

AU - Lund, Ole

AU - Løngren, Peter

AU - Mailund, Thomas

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 - Krogh, Anders

AU - Bolund, Lars

AU - Sørensen, Thorkild I. A.

AU - Pedersen, Oluf Borbye

AU - Gupta, Ramneek

AU - Rasmussen, Simon

AU - Besenbacher, Søren

AU - Børglum, Anders D.

AU - Wang, Jun

AU - Eiberg, Hans Rudolf Lytchoff

AU - Kristiansen, Karsten

AU - Brunak, Søren

AU - Schierup, Mikkel Heide

PY - 2017

Y1 - 2017

N2 - Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits1, 2, 3, 4. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly2, 5, 6, 7. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology4, 8, 9, 10, 11, 12, 13. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.

AB - Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits1, 2, 3, 4. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly2, 5, 6, 7. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology4, 8, 9, 10, 11, 12, 13. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.

U2 - 10.1038/nature23264

DO - 10.1038/nature23264

M3 - Letter

C2 - 28746312

VL - 548

SP - 87

EP - 91

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7665

ER -

ID: 183010683