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1. A draft human pangenome reference

Author

Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, and Benedict Paten

Subjects
Cancer Research, Multidisciplinary
Abstract

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 individuals1. 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.

Published
2023

2. Recombination between heterologous human acrocentric chromosomes

Author

Barcelona Supercomputing Center, Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey, Guarracino, Andrea, Buonaiuto, Silvia, Gomes de Lima, Leonardo, Potapova, Tamara, Rhie, Arang, Marco, Santiago, Barcelona Supercomputing Center, Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey, Guarracino, Andrea, Buonaiuto, Silvia, Gomes de Lima, Leonardo, Potapova, Tamara, Rhie, Arang, and Marco, Santiago

Abstract

The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembly of a human genome—the Telomere-to-Telomere Consortium’s CHM13 assembly (T2T-CHM13)—provided a model of their homology3, it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination6,7. The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations8, and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago9., Our work depends on the HPRC draft human pangenome resource established in the accompanying Article4, and we thank the production and assembly groups for their efforts in establishing this resource. This work used the computational resources of the UTHSC Octopus cluster and NIH HPC Biowulf cluster. We acknowledge support in maintaining these systems that was critical to our analyses. The authors thank M. Miller for the development of a graphical synopsis of our study (Fig. 5); and R. Williams and N. Soranzo for support and guidance in the design and discussion of our work. This work was supported, in part, by National Institutes of Health/NIDA U01DA047638 (E.G.), National Institutes of Health/NIGMS R01GM123489 (E.G.), NSF PPoSS Award no. 2118709 (E.G. and C.F.), the Tennessee Governor’s Chairs programme (C.F. and E.G.), National Institutes of Health/NCI R01CA266339 (T.P., L.G.d.L. and J.L.G.), and the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (A.R., S.K. and A.M.P.). We acknowledge support from Human Technopole (A.G.), Consiglio Nazionale delle Ricerche, Italy (S.B. and V.C.), and Stowers Institute for Medical Research (T.P., L.G.d.L., B.R. and J.L.G.)., Peer Reviewed, "Article signat per 13 autors/es: Andrea Guarracino, Silvia Buonaiuto, Leonardo Gomes de Lima, Tamara Potapova, Arang Rhie, Sergey Koren, Boris Rubinstein, Christian Fischer, Human Pangenome Reference Consortium, Jennifer L. Gerton, Adam M. Phillippy, Vincenza Colonna & Erik Garrison " Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. S, Postprint (published version)

Published
2023

3. A global reference for human genetic variation

Author

Colonna V. (1000 Genomes Project Consortium) Adam Auton, Gonçalo R Abecasis, David M Altshuler, Richard M Durbin, David R Bentley, Aravinda Chakravarti, Andrew G Clark, Peter Donnelly, Evan E Eichler, Paul Flicek, Stacey B Gabriel, Richard A Gibbs, Eric D Green, Matthew E Hurles, Bartha M Knoppers, Jan O Korbel, Eric S Lander, Charles Lee, Hans Lehrach, Elaine R Mardis, Gabor T Marth, Gil A McVean, Deborah A Nickerson, Jeanette P Schmidt, Stephen T Sherry, Jun Wang, Richard K Wilson, Eric Boerwinkle, Harsha Doddapaneni, Yi Han, Viktoriya Korchina, Christie Kovar, Sandra Lee, Donna Muzny, Jeffrey G Reid, Yiming Zhu, Yuqi Chang, Qiang Feng, Xiaodong Fang, Xiaosen Guo, Min Jian, Hui Jiang, Xin Jin, Tianming Lan, Guoqing Li, Jingxiang Li, Yingrui Li, Shengmao Liu, Xiao Liu, Yao Lu, Xuedi Ma, Meifang Tang, Bo Wang, Guangbiao Wang, Honglong Wu, Renhua Wu, Xun Xu, Ye Yin, Dandan Zhang, Wenwei Zhang, Jiao Zhao, Meiru Zhao, Xiaole Zheng, Namrata Gupta, Neda Gharani, Lorraine H Toji, Norman P Gerry, Alissa M Resch, Jonathan Barker, Laura Clarke, Laurent Gil, Sarah E Hunt, Gavin Kelman, Eugene Kulesha, Rasko Leinonen, William M McLaren, Rajesh Radhakrishnan, Asier Roa, Dmitriy Smirnov, Richard E Smith, Ian Streeter, Anja Thormann, Iliana Toneva, Brendan Vaughan, Xiangqun Zheng-Bradley, Russell Grocock, Sean Humphray, Terena James, Zoya Kingsbury, Ralf Sudbrak, Marcus W Albrecht, Vyacheslav S Amstislavskiy, Tatiana A Borodina, Matthias Lienhard, Florian Mertes, Marc Sultan, Bernd Timmermann, Marie-Laure Yaspo, Lucinda Fulton, Robert Fulton, Victor Ananiev, Zinaida Belaia, Dimitriy Beloslyudtsev, Nathan Bouk, Chao Chen, Deanna Church, Robert Cohen, Charles Cook, John Garner, Timothy Hefferon, Mikhail Kimelman, Chunlei Liu, John Lopez, Peter Meric, Chris O'Sullivan, Yuri Ostapchuk, Lon Phan, Sergiy Ponomarov, Valerie Schneider, Eugene Shekhtman, Karl Sirotkin, Douglas Slotta, Hua Zhang, Senduran Balasubramaniam, John Burton, Petr Danecek, Thomas M Keane, Anja Kolb-Kokocinski, Shane McCarthy, James Stalker, Michael Quail, Christopher J Davies, Jeremy Gollub, Teresa Webster, Brant Wong, Yiping Zhan, Adam Auton, Christopher L Campbell, Yu Kong, Anthony Marcketta, Fuli Yu, Lilian Antunes, Matthew Bainbridge, Aniko Sabo, Zhuoyi Huang, Lachlan J M Coin, Lin Fang, Qibin Li, Zhenyu Li, Haoxiang Lin, Binghang Liu, Ruibang Luo, Haojing Shao, Yinlong Xie, Chen Ye, Chang Yu, Fan Zhang, Hancheng Zheng, Hongmei Zhu, Can Alkan, Elif Dal, Fatma Kahveci, Erik P Garrison, Deniz Kural, Wan-Ping Lee, Wen Fung Leong, Michael Stromberg, Alistair N Ward, Jiantao Wu, Mengyao Zhang, Mark J Daly, Mark A DePristo, Robert E Handsaker, Eric Banks, Gaurav Bhatia, Guillermo Del Angel, Giulio Genovese, Heng Li, Seva Kashin, Steven A McCarroll, James C Nemesh, Ryan E Poplin, Seungtai C Yoon, Jayon Lihm, Vladimir Makarov, Srikanth Gottipati, Alon Keinan, Juan L Rodriguez-Flores, Tobias Rausch, Markus H Fritz, Adrian M Stütz, Kathryn Beal, Avik Datta, Javier Herrero, Graham R S Ritchie, Daniel Zerbino, Pardis C Sabeti, Ilya Shlyakhter, Stephen F Schaffner, Joseph Vitti, David N Cooper, Edward V Ball, Peter D Stenson, Bret Barnes, Markus Bauer, R Keira Cheetham, Anthony Cox, Michael Eberle, Scott Kahn, Lisa Murray, John Peden, Richard Shaw, Eimear E Kenny, Mark A Batzer, Miriam K Konkel, Jerilyn A Walker, Daniel G MacArthur, Monkol Lek, Ralf Herwig, Li Ding, Daniel C Koboldt, David Larson, Kai Ye, Simon Gravel, Anand Swaroop, Emily Chew, Tuuli Lappalainen, Yaniv Erlich, Melissa Gymrek, Thomas Frederick Willems, Jared T Simpson, Mark D Shriver, Jeffrey A Rosenfeld, Carlos D Bustamante, Stephen B Montgomery, Francisco M De La Vega, Jake K Byrnes, Andrew W Carroll, Marianne K DeGorter, Phil Lacroute, Brian K Maples, Alicia R Martin, Andres Moreno-Estrada, Suyash S Shringarpure, Fouad Zakharia, Eran Halperin, Yael Baran, Eliza Cerveira, Jaeho Hwang, Ankit Malhotra, Dariusz Plewczynski, Kamen Radew, Mallory Romanovitch, Chengsheng Zhang, Fiona C L Hyland, David W Craig, Alexis Christoforides, Nils Homer, Tyler Izatt, Ahmet A Kurdoglu, Shripad A Sinari, Kevin Squire, Chunlin Xiao, Jonathan Sebat, Danny Antaki, Madhusudan Gujral, Amina Noor, Kenny Ye, Esteban G Burchard, Ryan D Hernandez, Christopher R Gignoux, David Haussler, Sol J Katzman, W James Kent, Bryan Howie, Andres Ruiz-Linares, Emmanouil T Dermitzakis, Scott E Devine, Hyun Min Kang, Jeffrey M Kidd, Tom Blackwell, Sean Caron, Wei Chen, Sarah Emery, Lars Fritsche, Christian Fuchsberger, Goo Jun, Bingshan Li, Robert Lyons, Chris Scheller, Carlo Sidore, Shiya Song, Elzbieta Sliwerska, Daniel Taliun, Adrian Tan, Ryan Welch, Mary Kate Wing, Xiaowei Zhan, Philip Awadalla, Alan Hodgkinson, Yun Li, Xinghua Shi, Andrew Quitadamo, Gerton Lunter, Jonathan L Marchini, Simon Myers, Claire Churchhouse, Olivier Delaneau, Anjali Gupta-Hinch, Warren Kretzschmar, Zamin Iqbal, Iain Mathieson, Androniki Menelaou, Andy Rimmer, Dionysia K Xifara, Taras K Oleksyk, Yunxin Fu, Xiaoming Liu, Momiao Xiong, Lynn Jorde, David Witherspoon, Jinchuan Xing, Brian L Browning, Sharon R Browning, Fereydoun Hormozdiari, Peter H Sudmant, Ekta Khurana, Chris Tyler-Smith, Cornelis A Albers, Qasim Ayub, Yuan Chen, Vincenza Colonna, Luke Jostins, Klaudia Walter, Yali Xue, Mark B Gerstein, Alexej Abyzov, Suganthi Balasubramanian, Jieming Chen, Declan Clarke, Yao Fu, Arif O Harmanci, Mike Jin, Donghoon Lee, Jeremy Liu, Xinmeng Jasmine Mu, Jing Zhang, Yan Zhang, Chris Hartl, Khalid Shakir, Jeremiah Degenhardt, Sascha Meiers, Benjamin Raeder, Francesco Paolo Casale, Oliver Stegle, Eric-Wubbo Lameijer, Ira Hall, Vineet Bafna, Jacob Michaelson, Eugene J Gardner, Ryan E Mills, Gargi Dayama, Ken Chen, Xian Fan, Zechen Chong, Tenghui Chen, Mark J Chaisson, John Huddleston, Maika Malig, Bradley J Nelson, Nicholas F Parrish, Ben Blackburne, Sarah J Lindsay, Zemin Ning, Yujun Zhang, Hugo Lam, Cristina Sisu, Danny Challis, Uday S Evani, James Lu, Uma Nagaswamy, Jin Yu, Wangshen Li, Lukas Habegger, Haiyuan Yu, Fiona Cunningham, Ian Dunham, Kasper Lage, Jakob Berg Jespersen, Heiko Horn, Donghoon Kim, Rob Desalle, Apurva Narechania, Melissa A Wilson Sayres, Fernando L Mendez, G David Poznik, Peter A Underhill, Lachlan Coin, David Mittelman, Ruby Banerjee, Maria Cerezo, Thomas W Fitzgerald, Sandra Louzada, Andrea Massaia, Graham R Ritchie, Fengtang Yang, Divya Kalra, Walker Hale, Xu Dan, Kathleen C Barnes, Christine Beiswanger, Hongyu Cai, Hongzhi Cao, Brenna Henn, Danielle Jones, Jane S Kaye, Alastair Kent, Angeliki Kerasidou, Rasika Mathias, Pilar N Ossorio, Michael Parker, Charles N Rotimi, Charmaine D Royal, Karla Sandoval, Yeyang Su, Zhongming Tian, Sarah Tishkoff, Marc Via, Yuhong Wang, Huanming Yang, Ling Yang, Jiayong Zhu, Walter Bodmer, Gabriel Bedoya, Zhiming Cai, Yang Gao, Jiayou Chu, Leena Peltonen, Andres Garcia-Montero, Alberto Orfao, Julie Dutil, Juan C Martinez-Cruzado, Rasika A Mathias, Anselm Hennis, Harold Watson, Colin McKenzie, Firdausi Qadri, Regina LaRocque, Xiaoyan Deng, Danny Asogun, Onikepe Folarin, Christian Happi, Omonwunmi Omoniwa, Matt Stremlau, Ridhi Tariyal, Muminatou Jallow, Fatoumatta Sisay Joof, Tumani Corrah, Kirk Rockett, Dominic Kwiatkowski, Jaspal Kooner, Trân T?nh Hiên, Sarah J Dunstan, Nguyen Thuy Hang, Richard Fonnie, Robert Garry, Lansana Kanneh, Lina Moses, John Schieffelin, Donald S Grant, Carla Gallo, Giovanni Poletti, Danish Saleheen, Asif Rasheed, Lisa D Brooks, Adam L Felsenfeld, Jean E McEwen, Yekaterina Vaydylevich, Audrey Duncanson, Michael Dunn, Jeffery A Schloss, 1000 Genomes Project Consortium, Institute for Medical Engineering and Science, Broad Institute of MIT and Harvard, Lincoln Laboratory, Massachusetts Institute of Technology. Department of Biology, Gabriel, Stacey, Lander, Eric Steven, Daly, Mark J, Banks, Eric, Bhatia, Gaurav, Kashin, Seva, McCarroll, Steven A, Nemesh, James, Poplin, Ryan E., Sabeti, Pardis, Shlyakhter, Ilya, Schaffner, Stephen F, Vitti, Joseph, Gymrek, Melissa A, Hartler, Christina M., and Tariyal, Ridhi

Subjects
demography, genetic association, genotype, Human genomics, Genome-wide association study, Review, SUSCEPTIBILITY, DISEASE, polymorphism, 0302 clinical medicine, quantitative trait locus, INDEL Mutation, genetics, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), MUTATION, Exome sequencing, 0303 health sciences, public health, Sequence analysis, High-Throughput Nucleotide Sequencing, standard, Genomics, Reference Standards, Physical Chromosome Mapping, 3. Good health, priority journal, Science & Technology - Other Topics, BAYES FACTORS, Molecular Developmental Biology, Genotype, Genetics, Medical, Quantitative Trait Loci, DNA sequence, rare disease, human genetics, information processing, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, POPULATION HISTORY, human genome, Humans, retroposon, Genetic variability, human, GENOME-WIDE ASSOCIATION, 1000 Genomes Project, Demography, Science & Technology, ancestry, disease predisposition, Genetic Variation, MACULAR DEGENERATION, major clinical study, gene linkage disequilibrium, purl.org/pe-repo/ocde/ford#3.01.02 [https], Genetics, Population, 030217 neurology & neurosurgery, haplotype, Internationality, VARIANT, Datasets as Topic, Human genetic variation, COMPLEMENT FACTOR-H, single nucleotide polymorphism, genetic variability, Exome, chromosome map, Genetics, Variant Call Format, Genome, Multidisciplinary, 1000 Genomes Project Consortium, international cooperation, Multidisciplinary Sciences, standards, Disease Susceptibility, medical genetics, General Science & Technology, Population, Computational biology, Biology, gene frequency, Polymorphism, Single Nucleotide, high throughput sequencing, Rare Diseases, promoter region, MD Multidisciplinary, Genetic variation, QH426, 030304 developmental biology, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Genome, Human, population genetics, population structure, Sequence Analysis, DNA, gene structure, INDIVIDUALS, Haplotypes, Genome-Wide Association Study, purl.org/pe-repo/ocde/ford#1.06.07 [https]
Abstract

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies., Wellcome Trust (London, England) (Core Award 090532/Z/09/Z), Wellcome Trust (London, England) (Senior Investigator Award 095552/Z/11/Z ), Wellcome Trust (London, England) (WT095908), Wellcome Trust (London, England) (WT109497), Wellcome Trust (London, England) (WT098051), Wellcome Trust (London, England) (WT086084/Z/08/Z), Wellcome Trust (London, England) (WT100956/Z/13/Z ), Wellcome Trust (London, England) (WT097307), Wellcome Trust (London, England) (WT0855322/Z/08/Z ), Wellcome Trust (London, England) (WT090770/Z/09/Z ), Wellcome Trust (London, England) (Major Overseas program in Vietnam grant 089276/Z.09/Z), Medical Research Council (Great Britain) (grant G0801823), Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I02593X/1), Biotechnology and Biological Sciences Research Council (Great Britain) (grant BB/I021213/1), Zhongguo ke xue ji shu qing bao yan jiu suo. Office of 863 Programme of China (2012AA02A201), National Basic Research Program of China (2011CB809201), National Basic Research Program of China (2011CB809202), National Basic Research Program of China (2011CB809203), National Natural Science Foundation of China (31161130357), Shenzhen Municipal Government of China (grant ZYC201105170397A), Canadian Institutes of Health Research (grant 136855), Quebec Ministry of Economic Development, Innovation, and Exports (PSR-SIIRI-195), Germany. Bundesministerium für Bildung und Forschung (0315428A), Germany. Bundesministerium für Bildung und Forschung (01GS08201), Germany. Bundesministerium für Bildung und Forschung (BMBF-EPITREAT grant 0316190A), Deutsche Forschungsgemeinschaft (Emmy Noether Grant KO4037/1-1), Beatriu de Pinos Program (2006 BP-A 10144), Beatriu de Pinos Program (2009 BP-B 00274), Spanish National Institute for Health (grant PRB2 IPT13/0001-ISCIII-SGEFI/FEDER), Japan Society for the Promotion of Science (fellowship number PE13075), Marie Curie Actions Career Integration (grant 303772), Fonds National Suisse del la Recherche, SNSF, Scientifique (31003A_130342), National Center for Biotechnology Information (U.S.) (U54HG3067), National Center for Biotechnology Information (U.S.) (U54HG3273), National Center for Biotechnology Information (U.S.) (U01HG5211), National Center for Biotechnology Information (U.S.) (U54HG3079), National Center for Biotechnology Information (U.S.) (R01HG2898), National Center for Biotechnology Information (U.S.) (R01HG2385), National Center for Biotechnology Information (U.S.) (RC2HG5552), National Center for Biotechnology Information (U.S.) (U01HG6513), National Center for Biotechnology Information (U.S.) (U01HG5214), National Center for Biotechnology Information (U.S.) (U01HG5715), National Center for Biotechnology Information (U.S.) (U01HG5718), National Center for Biotechnology Information (U.S.) (U01HG5728), National Center for Biotechnology Information (U.S.) (U41HG7635), National Center for Biotechnology Information (U.S.) (U41HG7497), National Center for Biotechnology Information (U.S.) (R01HG4960), National Center for Biotechnology Information (U.S.) (R01HG5701), National Center for Biotechnology Information (U.S.) (R01HG5214), National Center for Biotechnology Information (U.S.) (R01HG6855), National Center for Biotechnology Information (U.S.) (R01HG7068), National Center for Biotechnology Information (U.S.) (R01HG7644), National Center for Biotechnology Information (U.S.) (DP2OD6514), National Center for Biotechnology Information (U.S.) (DP5OD9154), National Center for Biotechnology Information (U.S.) (R01CA166661), National Center for Biotechnology Information (U.S.) (R01CA172652), National Center for Biotechnology Information (U.S.) (P01GM99568), National Center for Biotechnology Information (U.S.) (R01GM59290), National Center for Biotechnology Information (U.S.) (R01GM104390), National Center for Biotechnology Information (U.S.) (T32GM7790), National Center for Biotechnology Information (U.S.) (R01HL87699), National Center for Biotechnology Information (U.S.) (R01HL104608), National Center for Biotechnology Information (U.S.) (T32HL94284), National Center for Biotechnology Information (U.S.) (HHSN268201100040C), National Center for Biotechnology Information (U.S.) (HHSN272201000025C), Lundbeck Foundation (grant R170-2014-1039, Simons Foundation (SFARI award SF51), National Science Foundation (U.S.) (Research Fellowship DGE-1147470)

Published
2015

4. Defining the boundaries of zebrafish developmental genetics

Author

Adam L. Felsenfeld

Subjects
Genetics, Embryonic Induction, Embryo, Nonmammalian, Genome, biology, Danio, Mutagenesis (molecular biology technique), Vertebrate, Chromosome Mapping, Gene Expression Regulation, Developmental, biology.organism_classification, Phenotype, Retina, Body plan, Evolutionary biology, biology.animal, Mutation, Animals, Zebrafish, Genomic organization
Abstract

The first systematic, functional screens to identify the genes involved in vertebrate embryogenesis have been completed in the zebrafish, Danio rerio. In an extraordinary issue of the journal Development, devoted entirely to the results of these screens, over 500 mutant loci, many with multiple alleles, are described and classified according to the phenotypes they produce. Each class defines a small number of genes that act together to determine the proper development of many features of vertebrate anatomy, from the determination of body plan to the development of discrete organs and cell types.

Published
1996

5. The fub-1 mutation blocks initial myofibril formation in zebrafish muscle pioneer cells

Author

Mark Curry, Adam L. Felsenfeld, and Charles B. Kimmel

Subjects
Myofilament, macromolecular substances, Biology, Protein filament, Myofibrils, Culture Techniques, Notochord, medicine, Myocyte, Animals, Molecular Biology, Actin, Zebrafish, Myogenesis, Muscles, Skeletal muscle, Cell Differentiation, Cell Biology, Anatomy, Actins, Cell biology, Microscopy, Electron, medicine.anatomical_structure, Mutation, Myofibril, Developmental Biology
Abstract

The earliest muscle in zebrafish arises from iterated sets of two to six cells in each somite, the muscle pioneers (MP). MP develop synchronously in young trunk myotomes adjacent to the notochord, precisely where the horizontal myoseptum will form. They elongate without cell fusion and differentiate hours earlier than surrounding cells, thus providing a simple and accessible system for in vivo study of myogenesis and muscle patterning. Before the MP form definitive myofibrils they assemble long bundles of actin-containing filaments, similar to "stress-fiber-like structures" reported by others. In fub-1 mutants, in which myofibrils are disorganized in all skeletal muscle cells, the MP appear and elongate normally, but ordered actin filament bundles are not seen. This defect could underlie the later myofibrillar ones, consistent with the proposal that actin filament bundles are essential for proper formation of the muscle contractile apparatus.

Published
1991

6. Mutations affecting skeletal muscle myofibril structure in the zebrafish

Author

Adam L. Felsenfeld, Charline Walker, Monte Westerfield, Charles Kimmel, and George Streisinger

Subjects
Electrophysiology, Microscopy, Electron, Muscles, Mutation, Animals, Electrophoresis, Gel, Two-Dimensional, Female, Genes, Lethal, Molecular Biology, Zebrafish, Developmental Biology
Abstract

We describe embryonic lethal mutations in the zebrafish, Brachydanio rerio, which affect organization of skeletal muscle myofibrils. The mutations, fub-l(b45) and fub-l( b126), were independently isolated from progeny of gamma-irradiated females. Each segregates as a single recessive gene; b45 is located about 23 map units from its centromere. The b126 mutation has a similar but slightly larger apparent gene–centromere distance and a less severe phenotype. The two mutations fail to complement, suggesting that they are allelic. Homozygous b45 mutant embryos are paralyzed, and their axial skeletal muscle cells are unstriated, containing severely disorganized myofibrillar components. Gel-electrophoretic comparisons of b45 mutant and wildtype muscle proteins failed to reveal absent or altered major myofibrillar proteins. Embryos genetically mosaic for b45 were also phenotypically mosaic, suggesting that the defect is cell-autonomous. We suggest that these mutations identify a gene required for proper organization of skeletal muscle myofibrils, and that the more severe mutation may represent a null allele.

Published
1990

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