Literature DB >> 30262473

Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification".

Chip Stewart1, Ignaty Leshchiner1, Julian Hess1, Gad Getz2,3,4.   

Abstract

Chen et al (Reports, 17 February 2017, p. 752) highlight an important problem of sequencing artifacts caused by DNA damage at the time of sample processing. However, their manuscript contains several errors that led the authors to incorrect conclusions. Moreover, the same sequencing artifacts were previously described and mitigated in The Cancer Genome Atlas and other published sequencing projects.
Copyright © 2018, American Association for the Advancement of Science.

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Year:  2018        PMID： 30262473      PMCID： PMC7350422          DOI： 10.1126/science.aas9824

Source DB:  PubMed          Journal:  Science        ISSN： 0036-8075            Impact factor:   47.728


  13 in total

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Journal:  Cancer Cell       Date:  2017-08-14       Impact factor: 31.743

2.  Integrated genomic characterization of papillary thyroid carcinoma.

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Journal:  Cell       Date:  2014-10-23       Impact factor: 41.582

3.  DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification.

Authors:  Lixin Chen; Pingfang Liu; Thomas C Evans; Laurence M Ettwiller
Journal:  Science       Date:  2017-02-17       Impact factor: 47.728

4.  DNA sequence context as a determinant of the quantity and chemistry of guanine oxidation produced by hydroxyl radicals and one-electron oxidants.

Authors:  Yelena Margolin; Vladimir Shafirovich; Nicholas E Geacintov; Michael S DeMott; Peter C Dedon
Journal:  J Biol Chem       Date:  2008-10-23       Impact factor: 5.157

5.  Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.

Authors:  Kyle Ellrott; Matthew H Bailey; Gordon Saksena; Kyle R Covington; Cyriac Kandoth; Chip Stewart; Julian Hess; Singer Ma; Kami E Chiotti; Michael McLellan; Heidi J Sofia; Carolyn Hutter; Gad Getz; David Wheeler; Li Ding
Journal:  Cell Syst       Date:  2018-03-28       Impact factor: 10.304

6.  Integrated genomic characterization of oesophageal carcinoma.

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Journal:  Nature       Date:  2017-01-04       Impact factor: 49.962

7.  Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.

Authors:  Marios Giannakis; Xinmeng Jasmine Mu; Sachet A Shukla; Zhi Rong Qian; Ofir Cohen; Reiko Nishihara; Samira Bahl; Yin Cao; Ali Amin-Mansour; Mai Yamauchi; Yasutaka Sukawa; Chip Stewart; Mara Rosenberg; Kosuke Mima; Kentaro Inamura; Katsuhiko Nosho; Jonathan A Nowak; Michael S Lawrence; Edward L Giovannucci; Andrew T Chan; Kimmie Ng; Jeffrey A Meyerhardt; Eliezer M Van Allen; Gad Getz; Stacey B Gabriel; Eric S Lander; Catherine J Wu; Charles S Fuchs; Shuji Ogino; Levi A Garraway
Journal:  Cell Rep       Date:  2016-10-18       Impact factor: 9.423

8.  Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation.

Authors:  Maura Costello; Trevor J Pugh; Timothy J Fennell; Chip Stewart; Lee Lichtenstein; James C Meldrim; Jennifer L Fostel; Dennis C Friedrich; Danielle Perrin; Danielle Dionne; Sharon Kim; Stacey B Gabriel; Eric S Lander; Sheila Fisher; Gad Getz
Journal:  Nucleic Acids Res       Date:  2013-01-08       Impact factor: 16.971

9.  The genetic landscape of high-risk neuroblastoma.

Authors:  Trevor J Pugh; Olena Morozova; Edward F Attiyeh; Shahab Asgharzadeh; Jun S Wei; Daniel Auclair; Scott L Carter; Kristian Cibulskis; Megan Hanna; Adam Kiezun; Jaegil Kim; Michael S Lawrence; Lee Lichenstein; Aaron McKenna; Chandra Sekhar Pedamallu; Alex H Ramos; Erica Shefler; Andrey Sivachenko; Carrie Sougnez; Chip Stewart; Adrian Ally; Inanc Birol; Readman Chiu; Richard D Corbett; Martin Hirst; Shaun D Jackman; Baljit Kamoh; Alireza Hadj Khodabakshi; Martin Krzywinski; Allan Lo; Richard A Moore; Karen L Mungall; Jenny Qian; Angela Tam; Nina Thiessen; Yongjun Zhao; Kristina A Cole; Maura Diamond; Sharon J Diskin; Yael P Mosse; Andrew C Wood; Lingyun Ji; Richard Sposto; Thomas Badgett; Wendy B London; Yvonne Moyer; Julie M Gastier-Foster; Malcolm A Smith; Jaime M Guidry Auvil; Daniela S Gerhard; Michael D Hogarty; Steven J M Jones; Eric S Lander; Stacey B Gabriel; Gad Getz; Robert C Seeger; Javed Khan; Marco A Marra; Matthew Meyerson; John M Maris
Journal:  Nat Genet       Date:  2013-01-20       Impact factor: 38.330

10.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.

Authors:  Kristian Cibulskis; Michael S Lawrence; Scott L Carter; Andrey Sivachenko; David Jaffe; Carrie Sougnez; Stacey Gabriel; Matthew Meyerson; Eric S Lander; Gad Getz
Journal:  Nat Biotechnol       Date:  2013-02-10       Impact factor: 54.908
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