Assembly of a pan-genome from deep sequencing of 910 humans of African descent.
Assembly of a pan-genome from deep sequencing of 910 humans of African descent.
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DOI：
10.1038/s41588-018-0273-y
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发表时间：
2019-01
期刊：
影响因子：
30.8
通讯作者：
Salzberg SL
中科院分区：
文献类型：
--
作者：
Sherman RM;Forman J;Antonescu V;Puiu D;Daya M;Rafaels N;Boorgula MP;Chavan S;Vergara C;Ortega VE;Levin AM;Eng C;Yazdanbakhsh M;Wilson JG;Marrugo J;Lange LA;Williams LK;Watson H;Ware LB;Olopade CO;Olopade O;Oliveira RR;Ober C;Nicolae DL;Meyers DA;Mayorga A;Knight-Madden J;Hartert T;Hansel NN;Foreman MG;Ford JG;Faruque MU;Dunston GM;Caraballo L;Burchard EG;Bleecker ER;Araujo MI;Herrera-Paz EF;Campbell M;Foster C;Taub MA;Beaty TH;Ruczinski I;Mathias RA;Barnes KC;Salzberg SL
我们使用了一个包含910名非洲裔个体的深度测序数据集来构建一组存在于这些个体中但在人类参考基因组中缺失的DNA序列。我们将来自这910名个体的1.19万亿条测序读段与参考基因组（GRCh38）进行比对，收集所有比对不上的读段，并将这些读段组装成连续的序列（重叠群）。然后我们将所有重叠群相互比较，以确定一组代表参考基因组中缺失的非洲泛基因组区域的独特序列。我们的分析显示，在非洲裔人群中存在的125,715个不同重叠群中共有296,485,284个碱基对，这表明非洲泛基因组比当前的人类参考基因组多包含约10%的DNA。尽管几乎所有这些序列的功能意义尚不清楚，但其中387个新的重叠群位于315个不同的蛋白质编码基因内，其余的似乎位于基因间区域。
从910名非洲裔个体组装泛基因组，确定了296.5Mb映射到125,715个不同重叠群的新DNA。这个非洲泛基因组比当前的人类参考基因组多包含约10%的DNA。
We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct a set of DNA sequences present in these individuals but missing from the reference human genome. We aligned 1.19 trillion reads from the 910 individuals to the reference genome (GRCh38), collected all reads that failed to align, and assembled these reads into contiguous sequences (contigs). We then compared all contigs to one another to identify a set of unique sequences representing regions of the African pan-genome missing from the reference genome. Our analysis revealed 296,485,284 bp in 125,715 distinct contigs present in the African-descended populations, demonstrating that the African pan-genome contains ~10% more DNA than the current human reference genome. Although the functional significance of nearly all of this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes while the rest appear to be intergenic. Assembly of a pan-genome from 910 humans of African descent identifies 296.5 Mb of novel DNA mapping to 125,715 distinct contigs. This African pan-genome contains ~10% more DNA than the current human reference genome.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
7
作者：
Huddleston J;Chaisson MJP;Steinberg KM;Warren W;Hoekzema K;Gordon D;Graves-Lindsay TA;Munson KM;Kronenberg ZN;Vives L;Peluso P;Boitano M;Chin CS;Korlach J;Wilson RK;Eichler EE
通讯作者：
Eichler EE
影响因子：
64.8
作者：
Mallick, Swapan;Li, Heng;Lipson, Mark;Mathieson, Iain;Gymrek, Melissa;Racimo, Fernando;Zhao, Mengyao;Chennagiri, Niru;Nordenfelt, Susanne;Tandon, Arti;Skoglund, Pontus;Lazaridis, Iosif;Sankararaman, Sriram;Fu, Qiaomei;Rohland, Nadin;Renaud, Gabriel;Erlich, Yaniv;Willems, Thomas;Gallo, Carla;Spence, Jeffrey P.;Song, Yun S.;Poletti, Giovanni;Balloux, Francois;van Driem, George;de Knijff, Peter;Romero, Irene Gallego;Jha, Aashish R.;Behar, Doron M.;Bravi, Claudio M.;Capelli, Cristian;Hervig, Tor;Moreno-Estrada, Andres;Posukh, Olga L.;Balanovska, Elena;Balanovsky, Oleg;Karachanak-Yankova, Sena;Sahakyan, Hovhannes;Toncheva, Draga;Yepiskoposyan, Levon;Tyler-Smith, Chris;Xue, Yali;Abdullah, M. Syafiq;Ruiz-Linares, Andres;Beall, Cynthia M.;Di Rienzo, Anna;Jeong, Choongwon;Starikovskaya, Elena B.;Metspalu, Ene;Parik, Juri;Villems, Richard;Henn, Brenna M.;Hodoglugil, Ugur;Mahley, Robert;Sajantila, Antti;Stamatoyannopoulos, George;Wee, Joseph T. S.;Khusainova, Rita;Khusnutdinova, Elza;Litvinov, Sergey;Ayodo, George;Comas, David;Hammer, Michael F.;Kivisild, Toomas;Klitz, William;Winkler, Cheryl A.;Labuda, Damian;Bamshad, Michael;Jorde, Lynn B.;Tishkoff, Sarah A.;Watkins, W. Scott;Metspalu, Mait;Dryomov, Stanislav;Sukernik, Rem;Singh, Lalji;Thangaraj, Kumarasamy;Paeaebo, Svante;Kelso, Janet;Patterson, Nick;Reich, David
通讯作者：
Reich, David
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
7
作者：
Schneider, Valerie A.;Graves-Lindsay, Tina;Church, Deanna M.
通讯作者：
Church, Deanna M.