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Wellcome Trust Sanger Institute

NonprofitCambridge, United Kingdom
About: Wellcome Trust Sanger Institute is a nonprofit organization based out in Cambridge, United Kingdom. It is known for research contribution in the topics: Population & Genome. The organization has 4009 authors who have published 9671 publications receiving 1224479 citations.


Papers
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Journal ArticleDOI
Arang Rhie1, Shane A. McCarthy2, Shane A. McCarthy3, Olivier Fedrigo4, Joana Damas5, Giulio Formenti4, Sergey Koren1, Marcela Uliano-Silva6, William Chow2, Arkarachai Fungtammasan, J. H. Kim7, Chul Hee Lee7, Byung June Ko7, Mark Chaisson8, Gregory Gedman4, Lindsey J. Cantin4, Françoise Thibaud-Nissen1, Leanne Haggerty9, Iliana Bista2, Iliana Bista3, Michelle Smith2, Bettina Haase4, Jacquelyn Mountcastle4, Sylke Winkler10, Sylke Winkler11, Sadye Paez4, Jason T. Howard, Sonja C. Vernes12, Sonja C. Vernes13, Sonja C. Vernes11, Tanya M. Lama14, Frank Grützner15, Wesley C. Warren16, Christopher N. Balakrishnan17, Dave W Burt18, Jimin George19, Matthew T. Biegler4, David Iorns, Andrew Digby, Daryl Eason, Bruce C. Robertson20, Taylor Edwards21, Mark Wilkinson22, George F. Turner23, Axel Meyer24, Andreas F. Kautt25, Andreas F. Kautt24, Paolo Franchini24, H. William Detrich26, Hannes Svardal27, Hannes Svardal28, Maximilian Wagner29, Gavin J. P. Naylor30, Martin Pippel11, Milan Malinsky2, Milan Malinsky31, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout32, Marlys L. Houck33, Ann C Misuraca33, Sarah B. Kingan34, Richard Hall34, Zev N. Kronenberg34, Ivan Sović34, Christopher Dunn34, Zemin Ning2, Alex Hastie, Joyce V. Lee, Siddarth Selvaraj, Richard E. Green32, Nicholas H. Putnam, Ivo Gut35, Jay Ghurye36, Erik Garrison32, Ying Sims2, Joanna Collins2, Sarah Pelan2, James Torrance2, Alan Tracey2, Jonathan Wood2, Robel E. Dagnew8, Dengfeng Guan3, Dengfeng Guan37, Sarah E. London38, David F. Clayton19, Claudio V. Mello39, Samantha R. Friedrich39, Peter V. Lovell39, Ekaterina Osipova11, Farooq O. Al-Ajli40, Farooq O. Al-Ajli41, Simona Secomandi42, Heebal Kim7, Constantina Theofanopoulou4, Michael Hiller43, Yang Zhou, Robert S. Harris44, Kateryna D. Makova44, Paul Medvedev44, Jinna Hoffman1, Patrick Masterson1, Karen Clark1, Fergal J. Martin9, Kevin L. Howe9, Paul Flicek9, Brian P. Walenz1, Woori Kwak, Hiram Clawson32, Mark Diekhans32, Luis R Nassar32, Benedict Paten32, Robert H. S. Kraus24, Robert H. S. Kraus11, Andrew J. Crawford45, M. Thomas P. Gilbert46, M. Thomas P. Gilbert47, Guojie Zhang, Byrappa Venkatesh48, Robert W. Murphy49, Klaus-Peter Koepfli50, Beth Shapiro32, Beth Shapiro51, Warren E. Johnson50, Warren E. Johnson52, Federica Di Palma53, Tomas Marques-Bonet, Emma C. Teeling54, Tandy Warnow55, Jennifer A. Marshall Graves56, Oliver A. Ryder57, Oliver A. Ryder33, David Haussler32, Stephen J. O'Brien58, Jonas Korlach34, Harris A. Lewin5, Kerstin Howe2, Eugene W. Myers11, Eugene W. Myers10, Richard Durbin2, Richard Durbin3, Adam M. Phillippy1, Erich D. Jarvis51, Erich D. Jarvis4 
National Institutes of Health1, Wellcome Trust Sanger Institute2, University of Cambridge3, Rockefeller University4, University of California, Davis5, Leibniz Association6, Seoul National University7, University of Southern California8, European Bioinformatics Institute9, Dresden University of Technology10, Max Planck Society11, University of St Andrews12, Radboud University Nijmegen13, University of Massachusetts Amherst14, University of Adelaide15, University of Missouri16, East Carolina University17, University of Queensland18, Clemson University19, University of Otago20, University of Arizona21, Natural History Museum22, Bangor University23, University of Konstanz24, Harvard University25, Northeastern University26, University of Antwerp27, National Museum of Natural History28, University of Graz29, University of Florida30, University of Basel31, University of California, Santa Cruz32, Zoological Society of San Diego33, Pacific Biosciences34, Pompeu Fabra University35, University of Maryland, College Park36, Harbin Institute of Technology37, University of Chicago38, Oregon Health & Science University39, Monash University Malaysia Campus40, Qatar Airways41, University of Milan42, Goethe University Frankfurt43, Pennsylvania State University44, University of Los Andes45, Norwegian University of Science and Technology46, University of Copenhagen47, Agency for Science, Technology and Research48, Royal Ontario Museum49, Smithsonian Institution50, Howard Hughes Medical Institute51, Walter Reed Army Institute of Research52, University of East Anglia53, University College Dublin54, University of Illinois at Urbana–Champaign55, La Trobe University56, University of California, San Diego57, Nova Southeastern University58
28 Apr 2021-Nature
TL;DR: The Vertebrate Genomes Project (VGP) as mentioned in this paper is an international effort to generate high quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

647 citations

Journal ArticleDOI
Richa Saxena1, Richa Saxena2, Claudia Langenberg, Toshiko Tanaka3  +170 moreInstitutions (52)
TL;DR: A meta-analysis of nine genome-wide association studies and a follow-up of 29 independent loci found three newly implicated loci to be associated with type 2 diabetes: GIPR, ADCY5 and VPS13C.
Abstract: Glucose levels 2 h after an oral glucose challenge are a clinical measure of glucose tolerance used in the diagnosis of type 2 diabetes. We report a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958-30,620). We identify variants at the GIPR locus associated with 2- h glucose level (rs10423928, beta (s.e.m.) = 0.09 (0.01) mmol/l per A allele, P = 2.0 x 10(-15)). The GIPR A-allele carriers also showed decreased insulin secretion (n = 22,492; insulinogenic index, P = 1.0 x 10(-17); ratio of insulin to glucose area under the curve, P = 1.3 x 10(-16)) and diminished incretin effect (n = 804; P = 4.3 x 10(-4)). We also identified variants at ADCY5 (rs2877716, P = 4.2 x 10(-16)), VPS13C (rs17271305, P = 4.1 x 10(-8)), GCKR (rs1260326, P = 7.1 x 10(-11)) and TCF7L2 (rs7903146, P = 4.2 x 10(-10)) associated with 2-h glucose. Of the three newly implicated loci (GIPR, ADCY5 and VPS13C), only ADCY5 was found to be associated with type 2 diabetes in collaborating studies (n = 35,869 cases, 89,798 controls, OR = 1.12, 95% CI 1.09-1.15, P = 4.8 x 10(-18)).

645 citations

Journal ArticleDOI
TL;DR: G&T-seq, a method for separating and sequencing genomic DNA and full-length mRNA from single cells, is described and cellular properties that could not be inferred from DNA or RNA sequencing alone are discovered.
Abstract: G&T-seq offers robust full-length transcript and whole-genome sequencing simultaneously from a single cell.

645 citations

Journal ArticleDOI
TL;DR: It is asserted that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote the understanding of human biology and advance the efforts to improve health.
Abstract: The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health.

643 citations


Authors

Showing all 4058 results

NameH-indexPapersCitations
Nicholas J. Wareham2121657204896
Gonçalo R. Abecasis179595230323
Panos Deloukas162410154018
Michael R. Stratton161443142586
David W. Johnson1602714140778
Michael John Owen1601110135795
Naveed Sattar1551326116368
Robert E. W. Hancock15277588481
Julian Parkhill149759104736
Nilesh J. Samani149779113545
Michael Conlon O'Donovan142736118857
Jian Yang1421818111166
Christof Koch141712105221
Andrew G. Clark140823123333
Stylianos E. Antonarakis13874693605
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202317
202270
2021836
2020810
2019854
2018764