Literature DB >> 27930809

ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.

Keiran M Raine1, Peter Van Loo1,2, David C Wedge1,3, David Jones1, Andrew Menzies1, Adam P Butler1, Jon W Teague1, Patrick Tarpey1, Serena Nik-Zainal1, Peter J Campbell1.   

Abstract

We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github.com/cancerit). This unit describes both 'one-shot' execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.
Copyright © 2016 John Wiley & Sons, Inc.

Entities:  

Keywords:  cancer; copy-number; sequencing; somatic

Mesh：

Year:  2016        PMID： 27930809      PMCID： PMC6097604          DOI： 10.1002/cpbi.17

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  8 in total

1.  Efficient storage of high throughput DNA sequencing data using reference-based compression.

Authors:  Markus Hsi-Yang Fritz; Rasko Leinonen; Guy Cochrane; Ewan Birney
Journal:  Genome Res       Date:  2011-01-18       Impact factor: 9.043

2.  Analyzing cancer samples with SNP arrays.

Authors:  Peter Van Loo; Gro Nilsen; Silje H Nordgard; Hans Kristian Moen Vollan; Anne-Lise Børresen-Dale; Vessela N Kristensen; Ole Christian Lingjærde
Journal:  Methods Mol Biol       Date:  2012

3.  Allele-specific copy number analysis of tumors.

Authors:  Peter Van Loo; Silje H Nordgard; Ole Christian Lingjærde; Hege G Russnes; Inga H Rye; Wei Sun; Victor J Weigman; Peter Marynen; Anders Zetterberg; Bjørn Naume; Charles M Perou; Anne-Lise Børresen-Dale; Vessela N Kristensen
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-13       Impact factor: 11.205

4.  A comprehensive catalogue of somatic mutations from a human cancer genome.

Authors:  Erin D Pleasance; R Keira Cheetham; Philip J Stephens; David J McBride; Sean J Humphray; Chris D Greenman; Ignacio Varela; Meng-Lay Lin; Gonzalo R Ordóñez; Graham R Bignell; Kai Ye; Julie Alipaz; Markus J Bauer; David Beare; Adam Butler; Richard J Carter; Lina Chen; Anthony J Cox; Sarah Edkins; Paula I Kokko-Gonzales; Niall A Gormley; Russell J Grocock; Christian D Haudenschild; Matthew M Hims; Terena James; Mingming Jia; Zoya Kingsbury; Catherine Leroy; John Marshall; Andrew Menzies; Laura J Mudie; Zemin Ning; Tom Royce; Ole B Schulz-Trieglaff; Anastassia Spiridou; Lucy A Stebbings; Lukasz Szajkowski; Jon Teague; David Williamson; Lynda Chin; Mark T Ross; Peter J Campbell; David R Bentley; P Andrew Futreal; Michael R Stratton
Journal:  Nature       Date:  2009-12-16       Impact factor: 49.962

5.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

6.  The variant call format and VCFtools.

Authors:  Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A Albers; Eric Banks; Mark A DePristo; Robert E Handsaker; Gerton Lunter; Gabor T Marth; Stephen T Sherry; Gilean McVean; Richard Durbin
Journal:  Bioinformatics       Date:  2011-06-07       Impact factor: 6.937

7.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

8.  Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Authors:  Serena Nik-Zainal; Helen Davies; Johan Staaf; Manasa Ramakrishna; Dominik Glodzik; Xueqing Zou; Inigo Martincorena; Ludmil B Alexandrov; Sancha Martin; David C Wedge; Peter Van Loo; Young Seok Ju; Marcel Smid; Arie B Brinkman; Sandro Morganella; Miriam R Aure; Ole Christian Lingjærde; Anita Langerød; Markus Ringnér; Sung-Min Ahn; Sandrine Boyault; Jane E Brock; Annegien Broeks; Adam Butler; Christine Desmedt; Luc Dirix; Serge Dronov; Aquila Fatima; John A Foekens; Moritz Gerstung; Gerrit K J Hooijer; Se Jin Jang; David R Jones; Hyung-Yong Kim; Tari A King; Savitri Krishnamurthy; Hee Jin Lee; Jeong-Yeon Lee; Yilong Li; Stuart McLaren; Andrew Menzies; Ville Mustonen; Sarah O'Meara; Iris Pauporté; Xavier Pivot; Colin A Purdie; Keiran Raine; Kamna Ramakrishnan; F Germán Rodríguez-González; Gilles Romieu; Anieta M Sieuwerts; Peter T Simpson; Rebecca Shepherd; Lucy Stebbings; Olafur A Stefansson; Jon Teague; Stefania Tommasi; Isabelle Treilleux; Gert G Van den Eynden; Peter Vermeulen; Anne Vincent-Salomon; Lucy Yates; Carlos Caldas; Laura van't Veer; Andrew Tutt; Stian Knappskog; Benita Kiat Tee Tan; Jos Jonkers; Åke Borg; Naoto T Ueno; Christos Sotiriou; Alain Viari; P Andrew Futreal; Peter J Campbell; Paul N Span; Steven Van Laere; Sunil R Lakhani; Jorunn E Eyfjord; Alastair M Thompson; Ewan Birney; Hendrik G Stunnenberg; Marc J van de Vijver; John W M Martens; Anne-Lise Børresen-Dale; Andrea L Richardson; Gu Kong; Gilles Thomas; Michael R Stratton
Journal:  Nature       Date:  2016-05-02       Impact factor: 49.962
  8 in total
  39 in total

1.  cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.

Authors:  David Jones; Keiran M Raine; Helen Davies; Patrick S Tarpey; Adam P Butler; Jon W Teague; Serena Nik-Zainal; Peter J Campbell
Journal:  Curr Protoc Bioinformatics       Date:  2016-12-08

2.  Somatic and Germline Variant Calling from Next-Generation Sequencing Data.

Authors:  Ti-Cheng Chang; Ke Xu; Zhongshan Cheng; Gang Wu
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

3.  Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study.

Authors:  Samantha Gadd; Vicki Huff; Andrew D Skol; Lindsay A Renfro; Conrad V Fernandez; Elizabeth A Mullen; Corbin D Jones; Katherine A Hoadley; Kai Lee Yap; Nilsa C Ramirez; Sheena Aris; Quy H Phung; Elizabeth J Perlman
Journal:  Cell Rep Med       Date:  2022-05-25

4.  Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells.

Authors:  Philip S Robinson; Laura E Thomas; Federico Abascal; Hyunchul Jung; Luke M R Harvey; Hannah D West; Sigurgeir Olafsson; Bernard C H Lee; Tim H H Coorens; Henry Lee-Six; Laura Butlin; Nicola Lander; Rebekah Truscott; Mathijs A Sanders; Stefanie V Lensing; Simon J A Buczacki; Rogier Ten Hoopen; Nicholas Coleman; Roxanne Brunton-Sim; Simon Rushbrook; Kourosh Saeb-Parsy; Fiona Lalloo; Peter J Campbell; Iñigo Martincorena; Julian R Sampson; Michael R Stratton
Journal:  Nat Commun       Date:  2022-07-08       Impact factor: 17.694

5.  Identification of recurrent noncoding mutations in B-cell lymphoma using capture Hi-C.

Authors:  Alex J Cornish; Phuc H Hoang; Sara E Dobbins; Philip J Law; Daniel Chubb; Giulia Orlando; Richard S Houlston
Journal:  Blood Adv       Date:  2019-01-08

6.  Development, maturation, and maintenance of human prostate inferred from somatic mutations.

Authors:  Sebastian Grossmann; Yvette Hooks; Laura Wilson; Luiza Moore; Laura O'Neill; Iñigo Martincorena; Thierry Voet; Michael R Stratton; Rakesh Heer; Peter J Campbell
Journal:  Cell Stem Cell       Date:  2021-03-02       Impact factor: 24.633

7.  Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

Authors:  Niedzica Camacho; Peter Van Loo; Sandra Edwards; Jonathan D Kay; Lucy Matthews; Kerstin Haase; Jeremy Clark; Nening Dennis; Sarah Thomas; Barbara Kremeyer; Jorge Zamora; Adam P Butler; Gunes Gundem; Sue Merson; Hayley Luxton; Steve Hawkins; Mohammed Ghori; Luke Marsden; Adam Lambert; Katalin Karaszi; Gill Pelvender; Charlie E Massie; Zsofia Kote-Jarai; Keiran Raine; David Jones; William J Howat; Steven Hazell; Naomi Livni; Cyril Fisher; Christopher Ogden; Pardeep Kumar; Alan Thompson; David Nicol; Erik Mayer; Tim Dudderidge; Yongwei Yu; Hongwei Zhang; Nimish C Shah; Vincent J Gnanapragasam; William Isaacs; Tapio Visakorpi; Freddie Hamdy; Dan Berney; Clare Verrill; Anne Y Warren; David C Wedge; Andrew G Lynch; Christopher S Foster; Yong Jie Lu; G Steven Bova; Hayley C Whitaker; Ultan McDermott; David E Neal; Rosalind Eeles; Colin S Cooper; Daniel S Brewer
Journal:  PLoS Genet       Date:  2017-09-25       Impact factor: 5.917

8.  Universal Patterns of Selection in Cancer and Somatic Tissues.

Authors:  Iñigo Martincorena; Keiran M Raine; Moritz Gerstung; Kevin J Dawson; Kerstin Haase; Peter Van Loo; Helen Davies; Michael R Stratton; Peter J Campbell
Journal:  Cell       Date:  2017-10-19       Impact factor: 41.582

9.  Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site.

Authors:  Joanna C Fowler; Charlotte King; Christopher Bryant; Michael W J Hall; Roshan Sood; Swee Hoe Ong; Eleanor Earp; David Fernandez-Antoran; Jonas Koeppel; Stefan C Dentro; David Shorthouse; Amer Durrani; Kate Fife; Edward Rytina; Doreen Milne; Amit Roshan; Krishnaa Mahububani; Kourosh Saeb-Parsy; Benjamin A Hall; Moritz Gerstung; Philip H Jones
Journal:  Cancer Discov       Date:  2020-10-21       Impact factor: 38.272

10.  Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer.

Authors:  Adam Pennycuick; Vitor H Teixeira; Khalid AbdulJabbar; Shan E Ahmed Raza; Tom Lund; Ayse U Akarca; Rachel Rosenthal; Lukas Kalinke; Deepak P Chandrasekharan; Christodoulos P Pipinikas; Henry Lee-Six; Robert E Hynds; Kate H C Gowers; Jake Y Henry; Fraser R Millar; Yeman B Hagos; Celine Denais; Mary Falzon; David A Moore; Sophia Antoniou; Pascal F Durrenberger; Andrew J Furness; Bernadette Carroll; Claire Marceaux; Marie-Liesse Asselin-Labat; William Larson; Courtney Betts; Lisa M Coussens; Ricky M Thakrar; Jeremy George; Charles Swanton; Christina Thirlwell; Peter J Campbell; Teresa Marafioti; Yinyin Yuan; Sergio A Quezada; Nicholas McGranahan; Sam M Janes
Journal:  Cancer Discov       Date:  2020-07-20       Impact factor: 38.272
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