Literature DB >> 26678382

cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing.

Keiran M Raine1, Jonathan Hinton1, Adam P Butler1, Jon W Teague1, Helen Davies1, Patrick Tarpey1, Serena Nik-Zainal1, Peter J Campbell1.   

Abstract

cgpPindel is a modified version of Pindel that is optimized for detecting somatic insertions and deletions (indels) in cancer genomes and other samples compared to a reference control. Post-hoc filters remove false positive calls, resulting in a high-quality dataset for downstream analysis. This unit provides concise instructions for both a simple 'one-shot' execution of cgpPindel and a more detailed approach suitable for large-scale compute farms.
Copyright © 2015 John Wiley & Sons, Inc.

Entities:  

Keywords:  Pindel; cancer; sequencing; somatic

Mesh：

Year:  2015        PMID： 26678382      PMCID： PMC6097606          DOI： 10.1002/0471250953.bi1507s52

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


  5 in total

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Journal:  Bioinformatics       Date:  2011-01-05       Impact factor: 6.937

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Journal:  Genome Res       Date:  2009-07-01       Impact factor: 9.043

3.  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

4.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

Authors:  Kai Ye; Marcel H Schulz; Quan Long; Rolf Apweiler; Zemin Ning
Journal:  Bioinformatics       Date:  2009-06-26       Impact factor: 6.937

5.  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
  5 in total
  38 in total

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Journal:  Leukemia       Date:  2017-12-06       Impact factor: 11.528

4.  Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis.

Authors:  Mia Petljak; Ludmil B Alexandrov; Jonathan S Brammeld; Stacey Price; David C Wedge; Sebastian Grossmann; Kevin J Dawson; Young Seok Ju; Francesco Iorio; Jose M C Tubio; Ching Chiek Koh; Ilias Georgakopoulos-Soares; Bernardo Rodríguez-Martín; Burçak Otlu; Sarah O'Meara; Adam P Butler; Andrew Menzies; Shriram G Bhosle; Keiran Raine; David R Jones; Jon W Teague; Kathryn Beal; Calli Latimer; Laura O'Neill; Jorge Zamora; Elizabeth Anderson; Nikita Patel; Mark Maddison; Bee Ling Ng; Jennifer Graham; Mathew J Garnett; Ultan McDermott; Serena Nik-Zainal; Peter J Campbell; Michael R Stratton
Journal:  Cell       Date:  2019-03-07       Impact factor: 41.582

5.  In situ CRISPR-Cas9 base editing for the development of genetically engineered mouse models of breast cancer.

Authors:  Stefano Annunziato; Catrin Lutz; Linda Henneman; Jinhyuk Bhin; Kim Wong; Bjørn Siteur; Bas van Gerwen; Renske de Korte-Grimmerink; Maria Paz Zafra; Emma M Schatoff; Anne Paulien Drenth; Eline van der Burg; Timo Eijkman; Siddhartha Mukherjee; Katharina Boroviak; Lodewyk Fa Wessels; Marieke van de Ven; Ivo J Huijbers; David J Adams; Lukas E Dow; Jos Jonkers
Journal:  EMBO J       Date:  2020-01-13       Impact factor: 11.598

6.  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

7.  Patterns of genomic change in residual disease after neoadjuvant chemotherapy for estrogen receptor-positive and HER2-negative breast cancer.

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8.  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
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9.  UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs.

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Journal:  Nat Genet       Date:  2018-05-07       Impact factor: 41.307

10.  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
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