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Institution

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
Jose M. C. Tubio1, Yang Li1, Young Seok Ju1, Inigo Martincorena1, Susanna L. Cooke1, Marta Tojo2, Gunes Gundem1, Christodoulos P. Pipinikas3, Jorge Zamora1, Keiran Raine1, Andrew Menzies1, Pablo Román-García1, Anthony Fullam1, Moritz Gerstung1, Adam Shlien1, Patrick S. Tarpey1, Elli Papaemmanuil1, Stian Knappskog4, Stian Knappskog1, Stian Knappskog5, Peter Van Loo1, Peter Van Loo6, Manasa Ramakrishna1, Helen Davies1, John Marshall1, David C. Wedge1, Jon W. Teague1, Adam Butler1, Serena Nik-Zainal7, Serena Nik-Zainal1, Ludmil B. Alexandrov1, Sam Behjati1, Lucy R. Yates1, Niccolo Bolli7, Niccolo Bolli1, Laura Mudie1, Claire Hardy1, Sancha Martin1, Stuart McLaren1, Sarah O’Meara1, Elizabeth Anderson1, Mark Maddison1, Stephen J. Gamble1, Christopher S. Foster8, Anne Y. Warren7, Hayley C. Whitaker7, Daniel Brewer9, Daniel Brewer10, Rosalind A. Eeles10, Colin Cooper9, Colin Cooper10, David E. Neal7, Andy G. Lynch7, Tapio Visakorpi11, William B. Isaacs12, Laura Van't Veer13, Carlos Caldas7, Christine Desmedt14, Christos Sotiriou14, Samuel Aparicio, John A. Foekens15, Jorunn E. Eyfjord16, Sunil R. Lakhani17, Sunil R. Lakhani18, Gilles Thomas19, Ola Myklebost20, Paul N. Span21, Anne Lise Børresen-Dale20, Andrea L. Richardson22, Marc J. van de Vijver, Anne Vincent-Salomon23, Gert Van den Eynden, Adrienne M. Flanagan3, Adrienne M. Flanagan24, P. Andrew Futreal25, P. Andrew Futreal1, Sam M. Janes3, G. Steven Bova11, Michael R. Stratton1, Ultan McDermott1, Peter J. Campbell1, Peter J. Campbell7 
01 Aug 2014-Science
TL;DR: It is found that 3′ transduction activity in a patient’s tumor was always associated with hypomethylation of that element, and in some cases transduction events can scatter exons, genes, and regulatory elements widely across the genome.
Abstract: Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome.

338 citations

Journal ArticleDOI
TL;DR: In this paper, the authors conducted genome-wide association studies to identify new loci associated with plasma levels, including coagulation factors VII (FVII), VIII (FVIII), and von Willebrand factor (vWF).
Abstract: Background— Plasma levels of coagulation factors VII (FVII), VIII (FVIII), and von Willebrand factor (vWF) influence risk of hemorrhage and thrombosis. We conducted genome-wide association studies to identify new loci associated with plasma levels. Methods and Results— The setting of the study included 5 community-based studies for discovery comprising 23 608 European-ancestry participants: Atherosclerosis Risk In Communities Study, Cardiovascular Health Study, British 1958 Birth Cohort, Framingham Heart Study, and Rotterdam Study. All subjects had genome-wide single-nucleotide polymorphism (SNP) scans and at least 1 phenotype measured: FVII activity/antigen, FVIII activity, and vWF antigen. Each study used its genotype data to impute to HapMap SNPs and independently conducted association analyses of hemostasis measures using an additive genetic model. Study findings were combined by meta-analysis. Replication was conducted in 7604 participants not in the discovery cohort. For FVII, 305 SNPs exceeded the ...

336 citations

Journal ArticleDOI
Luca Pagani1, Luca Pagani2, Luca Pagani3, Daniel Lawson4, Evelyn Jagoda5, Evelyn Jagoda3, Alexander Mörseburg3, Anders Eriksson3, Anders Eriksson6, Mario Mitt7, Florian Clemente3, Florian Clemente8, Georgi Hudjashov1, Georgi Hudjashov9, Georgi Hudjashov10, Michael DeGiorgio11, Lauri Saag1, Jeffrey D. Wall12, Alexia Cardona3, Reedik Mägi7, Melissa A. Wilson Sayres13, Melissa A. Wilson Sayres14, Sarah Kaewert3, Charlotte E. Inchley3, Christiana L. Scheib3, Mari Järve1, Monika Karmin10, Monika Karmin7, Monika Karmin1, Guy S. Jacobs15, Tiago Antao16, Florin Mircea Iliescu3, Alena Kushniarevich17, Alena Kushniarevich1, Qasim Ayub18, Chris Tyler-Smith18, Yali Xue18, Bayazit Yunusbayev1, Kristiina Tambets1, Chandana Basu Mallick1, Lehti Saag7, Elvira Pocheshkhova19, George Andriadze20, Craig Muller21, Michael C. Westaway22, David M. Lambert22, Grigor Zoraqi, Shahlo Turdikulova23, Dilbar Dalimova23, Zhaxylyk Sabitov24, Gazi Nurun Nahar Sultana25, Joseph Lachance26, Joseph Lachance27, Sarah A. Tishkoff27, Kuvat T. Momynaliev, Jainagul Isakova, Larisa Damba28, Marina Gubina28, Pagbajabyn Nymadawa29, Irina Evseeva30, L. A. Atramentova31, Olga Utevska31, François-Xavier Ricaut32, Nicolas Brucato32, Herawati Sudoyo33, Thierry Letellier32, Murray P. Cox9, Nikolay A. Barashkov34, Vedrana Škaro35, Lejla Mulahasanovic, Dragan Primorac, Hovhannes Sahakyan36, Hovhannes Sahakyan1, Maru Mormina37, Christina A. Eichstaedt3, Christina A. Eichstaedt38, Daria V. Lichman39, Daria V. Lichman28, S M Abdullah, Gyaneshwer Chaubey1, Joseph Wee, Evelin Mihailov7, A. S. Karunas40, Sergei Litvinov40, Sergei Litvinov1, Rita Khusainova40, N. V. Ekomasova40, V. L. Akhmetova, I. M. Khidiyatova40, Damir Marjanović41, Levon Yepiskoposyan36, Doron M. Behar1, Elena Balanovska28, Andres Metspalu7, Miroslava Derenko28, Boris Malyarchuk28, Mikhail Voevoda28, Mikhail Voevoda42, Mikhail Voevoda39, Sardana A. Fedorova34, Ludmila P. Osipova39, Ludmila P. Osipova28, Marta Mirazón Lahr3, Pascale Gerbault43, Matthew Leavesley44, Matthew Leavesley45, Andrea Bamberg Migliano43, Michael D. Petraglia46, Oleg Balanovsky28, Elza Khusnutdinova40, Ene Metspalu1, Ene Metspalu7, Mark G. Thomas43, Andrea Manica3, Rasmus Nielsen47, Richard Villems48, Richard Villems7, Richard Villems1, Eske Willerslev21, Toomas Kivisild1, Toomas Kivisild3, Mait Metspalu1 
13 Oct 2016-Nature
TL;DR: A genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa earlier than 75,000 years ago is found.
Abstract: High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

336 citations

Journal ArticleDOI
24 Mar 2016-Cell
TL;DR: The results indicate that heterogeneous gene expression, as early as the 4-cell stage, initiates cell-fate decisions by modulating the balance of pluripotency and differentiation.

335 citations

Journal ArticleDOI
TL;DR: In many tumors, the coding sequence of 518 protein kinases was examined, and a few had numerous somatic mutations with distinctive patterns indicative of either a mutator phenotype or a past exposure.
Abstract: We examined the coding sequence of 518 protein kinases, approximately 1.3 Mb of DNA per sample, in 25 breast cancers. In many tumors, we detected no somatic mutations. But a few had numerous somatic mutations with distinctive patterns indicative of either a mutator phenotype or a past exposure.

335 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