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A draft human pangenome reference
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals(1). These assemblies cover more than 99% of the expected sequence in each genome and are more t...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172123/ https://www.ncbi.nlm.nih.gov/pubmed/37165242 http://dx.doi.org/10.1038/s41586-023-05896-x |
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author | Liao, Wen-Wei Asri, Mobin Ebler, Jana Doerr, Daniel Haukness, Marina Hickey, Glenn Lu, Shuangjia Lucas, Julian K. Monlong, Jean Abel, Haley J. Buonaiuto, Silvia Chang, Xian H. Cheng, Haoyu Chu, Justin Colonna, Vincenza Eizenga, Jordan M. Feng, Xiaowen Fischer, Christian Fulton, Robert S. Garg, Shilpa Groza, Cristian Guarracino, Andrea Harvey, William T. Heumos, Simon Howe, Kerstin Jain, Miten Lu, Tsung-Yu Markello, Charles Martin, Fergal J. Mitchell, Matthew W. Munson, Katherine M. Mwaniki, Moses Njagi Novak, Adam M. Olsen, Hugh E. Pesout, Trevor Porubsky, David Prins, Pjotr Sibbesen, Jonas A. Sirén, Jouni Tomlinson, Chad Villani, Flavia Vollger, Mitchell R. Antonacci-Fulton, Lucinda L. Baid, Gunjan Baker, Carl A. Belyaeva, Anastasiya Billis, Konstantinos Carroll, Andrew Chang, Pi-Chuan Cody, Sarah Cook, Daniel E. Cook-Deegan, Robert M. Cornejo, Omar E. Diekhans, Mark Ebert, Peter Fairley, Susan Fedrigo, Olivier Felsenfeld, Adam L. Formenti, Giulio Frankish, Adam Gao, Yan Garrison, Nanibaa’ A. Giron, Carlos Garcia Green, Richard E. Haggerty, Leanne Hoekzema, Kendra Hourlier, Thibaut Ji, Hanlee P. Kenny, Eimear E. Koenig, Barbara A. Kolesnikov, Alexey Korbel, Jan O. Kordosky, Jennifer Koren, Sergey Lee, HoJoon Lewis, Alexandra P. Magalhães, Hugo Marco-Sola, Santiago Marijon, Pierre McCartney, Ann McDaniel, Jennifer Mountcastle, Jacquelyn Nattestad, Maria Nurk, Sergey Olson, Nathan D. Popejoy, Alice B. Puiu, Daniela Rautiainen, Mikko Regier, Allison A. Rhie, Arang Sacco, Samuel Sanders, Ashley D. Schneider, Valerie A. Schultz, Baergen I. Shafin, Kishwar Smith, Michael W. Sofia, Heidi J. Abou Tayoun, Ahmad N. Thibaud-Nissen, Françoise Tricomi, Francesca Floriana Wagner, Justin Walenz, Brian Wood, Jonathan M. D. Zimin, Aleksey V. Bourque, Guillaume Chaisson, Mark J. P. Flicek, Paul Phillippy, Adam M. Zook, Justin M. Eichler, Evan E. Haussler, David Wang, Ting Jarvis, Erich D. Miga, Karen H. Garrison, Erik Marschall, Tobias Hall, Ira M. Li, Heng Paten, Benedict |
author_facet | Liao, Wen-Wei Asri, Mobin Ebler, Jana Doerr, Daniel Haukness, Marina Hickey, Glenn Lu, Shuangjia Lucas, Julian K. Monlong, Jean Abel, Haley J. Buonaiuto, Silvia Chang, Xian H. Cheng, Haoyu Chu, Justin Colonna, Vincenza Eizenga, Jordan M. Feng, Xiaowen Fischer, Christian Fulton, Robert S. Garg, Shilpa Groza, Cristian Guarracino, Andrea Harvey, William T. Heumos, Simon Howe, Kerstin Jain, Miten Lu, Tsung-Yu Markello, Charles Martin, Fergal J. Mitchell, Matthew W. Munson, Katherine M. Mwaniki, Moses Njagi Novak, Adam M. Olsen, Hugh E. Pesout, Trevor Porubsky, David Prins, Pjotr Sibbesen, Jonas A. Sirén, Jouni Tomlinson, Chad Villani, Flavia Vollger, Mitchell R. Antonacci-Fulton, Lucinda L. Baid, Gunjan Baker, Carl A. Belyaeva, Anastasiya Billis, Konstantinos Carroll, Andrew Chang, Pi-Chuan Cody, Sarah Cook, Daniel E. Cook-Deegan, Robert M. Cornejo, Omar E. Diekhans, Mark Ebert, Peter Fairley, Susan Fedrigo, Olivier Felsenfeld, Adam L. Formenti, Giulio Frankish, Adam Gao, Yan Garrison, Nanibaa’ A. Giron, Carlos Garcia Green, Richard E. Haggerty, Leanne Hoekzema, Kendra Hourlier, Thibaut Ji, Hanlee P. Kenny, Eimear E. Koenig, Barbara A. Kolesnikov, Alexey Korbel, Jan O. Kordosky, Jennifer Koren, Sergey Lee, HoJoon Lewis, Alexandra P. Magalhães, Hugo Marco-Sola, Santiago Marijon, Pierre McCartney, Ann McDaniel, Jennifer Mountcastle, Jacquelyn Nattestad, Maria Nurk, Sergey Olson, Nathan D. Popejoy, Alice B. Puiu, Daniela Rautiainen, Mikko Regier, Allison A. Rhie, Arang Sacco, Samuel Sanders, Ashley D. Schneider, Valerie A. Schultz, Baergen I. Shafin, Kishwar Smith, Michael W. Sofia, Heidi J. Abou Tayoun, Ahmad N. Thibaud-Nissen, Françoise Tricomi, Francesca Floriana Wagner, Justin Walenz, Brian Wood, Jonathan M. D. Zimin, Aleksey V. Bourque, Guillaume Chaisson, Mark J. P. Flicek, Paul Phillippy, Adam M. Zook, Justin M. Eichler, Evan E. Haussler, David Wang, Ting Jarvis, Erich D. Miga, Karen H. Garrison, Erik Marschall, Tobias Hall, Ira M. Li, Heng Paten, Benedict |
author_sort | Liao, Wen-Wei |
collection | PubMed |
description | Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals(1). These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample. |
format | Online Article Text |
id | pubmed-10172123 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-101721232023-05-12 A draft human pangenome reference Liao, Wen-Wei Asri, Mobin Ebler, Jana Doerr, Daniel Haukness, Marina Hickey, Glenn Lu, Shuangjia Lucas, Julian K. Monlong, Jean Abel, Haley J. Buonaiuto, Silvia Chang, Xian H. Cheng, Haoyu Chu, Justin Colonna, Vincenza Eizenga, Jordan M. Feng, Xiaowen Fischer, Christian Fulton, Robert S. Garg, Shilpa Groza, Cristian Guarracino, Andrea Harvey, William T. Heumos, Simon Howe, Kerstin Jain, Miten Lu, Tsung-Yu Markello, Charles Martin, Fergal J. Mitchell, Matthew W. Munson, Katherine M. Mwaniki, Moses Njagi Novak, Adam M. Olsen, Hugh E. Pesout, Trevor Porubsky, David Prins, Pjotr Sibbesen, Jonas A. Sirén, Jouni Tomlinson, Chad Villani, Flavia Vollger, Mitchell R. Antonacci-Fulton, Lucinda L. Baid, Gunjan Baker, Carl A. Belyaeva, Anastasiya Billis, Konstantinos Carroll, Andrew Chang, Pi-Chuan Cody, Sarah Cook, Daniel E. Cook-Deegan, Robert M. Cornejo, Omar E. Diekhans, Mark Ebert, Peter Fairley, Susan Fedrigo, Olivier Felsenfeld, Adam L. Formenti, Giulio Frankish, Adam Gao, Yan Garrison, Nanibaa’ A. Giron, Carlos Garcia Green, Richard E. Haggerty, Leanne Hoekzema, Kendra Hourlier, Thibaut Ji, Hanlee P. Kenny, Eimear E. Koenig, Barbara A. Kolesnikov, Alexey Korbel, Jan O. Kordosky, Jennifer Koren, Sergey Lee, HoJoon Lewis, Alexandra P. Magalhães, Hugo Marco-Sola, Santiago Marijon, Pierre McCartney, Ann McDaniel, Jennifer Mountcastle, Jacquelyn Nattestad, Maria Nurk, Sergey Olson, Nathan D. Popejoy, Alice B. Puiu, Daniela Rautiainen, Mikko Regier, Allison A. Rhie, Arang Sacco, Samuel Sanders, Ashley D. Schneider, Valerie A. Schultz, Baergen I. Shafin, Kishwar Smith, Michael W. Sofia, Heidi J. Abou Tayoun, Ahmad N. Thibaud-Nissen, Françoise Tricomi, Francesca Floriana Wagner, Justin Walenz, Brian Wood, Jonathan M. D. Zimin, Aleksey V. Bourque, Guillaume Chaisson, Mark J. P. Flicek, Paul Phillippy, Adam M. Zook, Justin M. Eichler, Evan E. Haussler, David Wang, Ting Jarvis, Erich D. Miga, Karen H. Garrison, Erik Marschall, Tobias Hall, Ira M. Li, Heng Paten, Benedict Nature Article Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals(1). These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample. Nature Publishing Group UK 2023-05-10 2023 /pmc/articles/PMC10172123/ /pubmed/37165242 http://dx.doi.org/10.1038/s41586-023-05896-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Liao, Wen-Wei Asri, Mobin Ebler, Jana Doerr, Daniel Haukness, Marina Hickey, Glenn Lu, Shuangjia Lucas, Julian K. Monlong, Jean Abel, Haley J. Buonaiuto, Silvia Chang, Xian H. Cheng, Haoyu Chu, Justin Colonna, Vincenza Eizenga, Jordan M. Feng, Xiaowen Fischer, Christian Fulton, Robert S. Garg, Shilpa Groza, Cristian Guarracino, Andrea Harvey, William T. Heumos, Simon Howe, Kerstin Jain, Miten Lu, Tsung-Yu Markello, Charles Martin, Fergal J. Mitchell, Matthew W. Munson, Katherine M. Mwaniki, Moses Njagi Novak, Adam M. Olsen, Hugh E. Pesout, Trevor Porubsky, David Prins, Pjotr Sibbesen, Jonas A. Sirén, Jouni Tomlinson, Chad Villani, Flavia Vollger, Mitchell R. Antonacci-Fulton, Lucinda L. Baid, Gunjan Baker, Carl A. Belyaeva, Anastasiya Billis, Konstantinos Carroll, Andrew Chang, Pi-Chuan Cody, Sarah Cook, Daniel E. Cook-Deegan, Robert M. Cornejo, Omar E. Diekhans, Mark Ebert, Peter Fairley, Susan Fedrigo, Olivier Felsenfeld, Adam L. Formenti, Giulio Frankish, Adam Gao, Yan Garrison, Nanibaa’ A. Giron, Carlos Garcia Green, Richard E. Haggerty, Leanne Hoekzema, Kendra Hourlier, Thibaut Ji, Hanlee P. Kenny, Eimear E. Koenig, Barbara A. Kolesnikov, Alexey Korbel, Jan O. Kordosky, Jennifer Koren, Sergey Lee, HoJoon Lewis, Alexandra P. Magalhães, Hugo Marco-Sola, Santiago Marijon, Pierre McCartney, Ann McDaniel, Jennifer Mountcastle, Jacquelyn Nattestad, Maria Nurk, Sergey Olson, Nathan D. Popejoy, Alice B. Puiu, Daniela Rautiainen, Mikko Regier, Allison A. Rhie, Arang Sacco, Samuel Sanders, Ashley D. Schneider, Valerie A. Schultz, Baergen I. Shafin, Kishwar Smith, Michael W. Sofia, Heidi J. Abou Tayoun, Ahmad N. Thibaud-Nissen, Françoise Tricomi, Francesca Floriana Wagner, Justin Walenz, Brian Wood, Jonathan M. D. Zimin, Aleksey V. Bourque, Guillaume Chaisson, Mark J. P. Flicek, Paul Phillippy, Adam M. Zook, Justin M. Eichler, Evan E. Haussler, David Wang, Ting Jarvis, Erich D. Miga, Karen H. Garrison, Erik Marschall, Tobias Hall, Ira M. Li, Heng Paten, Benedict A draft human pangenome reference |
title | A draft human pangenome reference |
title_full | A draft human pangenome reference |
title_fullStr | A draft human pangenome reference |
title_full_unstemmed | A draft human pangenome reference |
title_short | A draft human pangenome reference |
title_sort | draft human pangenome reference |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172123/ https://www.ncbi.nlm.nih.gov/pubmed/37165242 http://dx.doi.org/10.1038/s41586-023-05896-x |
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