A draft human pangenome reference.
A draft human pangenome reference.
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DOI：
10.1038/s41586-023-05896-x
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发表时间：
2023-05
期刊：
影响因子：
64.8
通讯作者：
Paten, Benedict
中科院分区：
文献类型：
--
作者：
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.;Siren, 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.;Magalhaes, 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, Francoise;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.;Erik, Garrison;Tobias, Marschall;Ira, M. Hall;Li, Heng;Paten, Benedict
在这里，人类泛基因组参考联盟提出了人类泛基因组参考的初稿。泛基因组包含47个来自一组遗传多样性个体的定相二倍体组装体。这些组件覆盖了每个基因组中超过99%的预期序列，并且在结构和碱基对水平上的准确度超过99%。基于组装的比对，我们生成了一个泛基因组草案，该草案捕获了已知的变体和单倍型，并揭示了结构复杂基因座处的新等位基因。我们还增加了1.19亿个碱基对的常染色质多态性序列和1,115个相对于现有参考GRCh 38的基因重复。大约9000万个额外的碱基对来自结构变异。与基于GRCh 38的工作流程相比，使用我们的pangenome草案分析短读数据将小变异发现错误减少了34%，并将每个单倍型检测到的结构变异数量增加了104%，这使得每个样本的绝大多数结构变异等位基因的分型成为可能。人类泛基因组参考联盟（Human Pangenome Reference Consortium）提出并公开了人类泛基因组的初步草案;该草案包含来自47个祖先不同的个体的94个从头单倍型组装。
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. 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. An initial draft of the human pangenome is presented and made publicly available by the Human Pangenome Reference Consortium; the draft contains 94 de novo haplotype assemblies from 47 ancestrally diverse individuals.
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影响因子：
12.3
作者：
Garg S
通讯作者：
Garg S
影响因子：
64.8
作者：
Armstrong J;Hickey G;Diekhans M;Fiddes IT;Novak AM;Deran A;Fang Q;Xie D;Feng S;Stiller J;Genereux D;Johnson J;Marinescu VD;Alföldi J;Harris RS;Lindblad-Toh K;Haussler D;Karlsson E;Jarvis ED;Zhang G;Paten B
通讯作者：
Paten B
影响因子：
48
作者：
Cheng H;Concepcion GT;Feng X;Zhang H;Li H
通讯作者：
Li H
DOI：
10.1146/annurev-genom-120219-080406
发表时间：
2020-08-31
影响因子：
8.7
作者：
Eizenga JM;Novak AM;Sibbesen JA;Heumos S;Ghaffaari A;Hickey G;Chang X;Seaman JD;Rounthwaite R;Ebler J;Rautiainen M;Garg S;Paten B;Marschall T;Sirén J;Garrison E
通讯作者：
Garrison E
唾液淀粉酶基因的低拷贝数易于肥胖。
影响因子：
30.8
作者：
Falchi M;El-Sayed Moustafa JS;Takousis P;Pesce F;Bonnefond A;Andersson-Assarsson JC;Sudmant PH;Dorajoo R;Al-Shafai MN;Bottolo L;Ozdemir E;So HC;Davies RW;Patrice A;Dent R;Mangino M;Hysi PG;Dechaume A;Huyvaert M;Skinner J;Pigeyre M;Caiazzo R;Raverdy V;Vaillant E;Field S;Balkau B;Marre M;Visvikis-Siest S;Weill J;Poulain-Godefroy O;Jacobson P;Sjostrom L;Hammond CJ;Deloukas P;Sham PC;McPherson R;Lee J;Tai ES;Sladek R;Carlsson LM;Walley A;Eichler EE;Pattou F;Spector TD;Froguel P
通讯作者：
Froguel P