Literature DB >> 28968631

Computational approaches for discovery of mutational signatures in cancer.

Adrian Baez-Ortega1, Kevin Gori1.   

Abstract

The accumulation of somatic mutations in a genome is the result of the activity of one or more mutagenic processes, each of which leaves its own imprint. The study of these DNA fingerprints, termed mutational signatures, holds important potential for furthering our understanding of the causes and evolution of cancer, and can provide insights of relevance for cancer prevention and treatment. In this review, we focus our attention on the mathematical models and computational techniques that have driven recent advances in the field.

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Year:  2019        PMID: 28968631      PMCID: PMC6357558          DOI: 10.1093/bib/bbx082

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  81 in total

Review 1.  Errors in DNA replication as a basis of malignant changes.

Authors:  L A Loeb; C F Springgate; N Battula
Journal:  Cancer Res       Date:  1974-09       Impact factor: 12.701

Review 2.  Evolution of the cancer genome.

Authors:  Lucy R Yates; Peter J Campbell
Journal:  Nat Rev Genet       Date:  2012-10-09       Impact factor: 53.242

3.  Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes.

Authors:  M Krawczak; E V Ball; D N Cooper
Journal:  Am J Hum Genet       Date:  1998-08       Impact factor: 11.025

4.  Genomic landscape of non-small cell lung cancer in smokers and never-smokers.

Authors:  Ramaswamy Govindan; Li Ding; Malachi Griffith; Janakiraman Subramanian; Nathan D Dees; Krishna L Kanchi; Christopher A Maher; Robert Fulton; Lucinda Fulton; John Wallis; Ken Chen; Jason Walker; Sandra McDonald; Ron Bose; David Ornitz; Donghai Xiong; Ming You; David J Dooling; Mark Watson; Elaine R Mardis; Richard K Wilson
Journal:  Cell       Date:  2012-09-14       Impact factor: 41.582

5.  Clonal selection and double-hit events involving tumor suppressor genes underlie relapse in myeloma.

Authors:  Niels Weinhold; Cody Ashby; Leo Rasche; Shweta S Chavan; Caleb Stein; Owen W Stephens; Ruslana Tytarenko; Michael A Bauer; Tobias Meissner; Shayu Deshpande; Purvi H Patel; Timea Buzder; Gabor Molnar; Erich A Peterson; Frits van Rhee; Maurizio Zangari; Sharmilan Thanendrarajan; Carolina Schinke; Erming Tian; Joshua Epstein; Bart Barlogie; Faith E Davies; Christoph J Heuck; Brian A Walker; Gareth J Morgan
Journal:  Blood       Date:  2016-08-11       Impact factor: 22.113

6.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

7.  DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer.

Authors:  Nnennaya Kanu; Maria Antonietta Cerone; Gerald Goh; Lykourgos-Panagiotis Zalmas; Jirina Bartkova; Michelle Dietzen; Nicholas McGranahan; Rebecca Rogers; Emily K Law; Irina Gromova; Maik Kschischo; Michael I Walton; Olivia W Rossanese; Jiri Bartek; Reuben S Harris; Subramanian Venkatesan; Charles Swanton
Journal:  Genome Biol       Date:  2016-09-15       Impact factor: 13.583

8.  Clock-like mutational processes in human somatic cells.

Authors:  Ludmil B Alexandrov; Philip H Jones; David C Wedge; Julian E Sale; Peter J Campbell; Serena Nik-Zainal; Michael R Stratton
Journal:  Nat Genet       Date:  2015-11-09       Impact factor: 38.330

Review 9.  Mutational signatures: the patterns of somatic mutations hidden in cancer genomes.

Authors:  Ludmil B Alexandrov; Michael R Stratton
Journal:  Curr Opin Genet Dev       Date:  2013-12-29       Impact factor: 5.578

10.  A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures.

Authors:  Yuichi Shiraishi; Georg Tremmel; Satoru Miyano; Matthew Stephens
Journal:  PLoS Genet       Date:  2015-12-02       Impact factor: 5.917

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  10 in total

Review 1.  Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance.

Authors:  Hanane Omichessan; Gianluca Severi; Vittorio Perduca
Journal:  PLoS One       Date:  2019-09-12       Impact factor: 3.240

2.  Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma.

Authors:  J Nicholas Fisk; Amandeep R Mahal; Alex Dornburg; Stephen G Gaffney; Sanjay Aneja; Joseph N Contessa; David Rimm; James B Yu; Jeffrey P Townsend
Journal:  Cancer Lett       Date:  2021-11-12       Impact factor: 8.679

3.  SUITOR: Selecting the number of mutational signatures through cross-validation.

Authors:  Donghyuk Lee; Difei Wang; Xiaohong R Yang; Jianxin Shi; Maria Teresa Landi; Bin Zhu
Journal:  PLoS Comput Biol       Date:  2022-04-04       Impact factor: 4.779

4.  Somatic evolution and global expansion of an ancient transmissible cancer lineage.

Authors:  Kevin Gori; Andrea Strakova; Adrian Baez-Ortega; Janice L Allen; Karen M Allum; Leontine Bansse-Issa; Thinlay N Bhutia; Jocelyn L Bisson; Cristóbal Briceño; Artemio Castillo Domracheva; Anne M Corrigan; Hugh R Cran; Jane T Crawford; Eric Davis; Karina F de Castro; Andrigo B de Nardi; Anna P de Vos; Laura Delgadillo Keenan; Edward M Donelan; Adela R Espinoza Huerta; Ibikunle A Faramade; Mohammed Fazil; Eleni Fotopoulou; Skye N Fruean; Fanny Gallardo-Arrieta; Olga Glebova; Pagona G Gouletsou; Rodrigo F Häfelin Manrique; Joaquim J G P Henriques; Rodrigo S Horta; Natalia Ignatenko; Yaghouba Kane; Cathy King; Debbie Koenig; Ada Krupa; Steven J Kruzeniski; Young-Mi Kwon; Marta Lanza-Perea; Mihran Lazyan; Adriana M Lopez Quintana; Thibault Losfelt; Gabriele Marino; Simón Martínez Castañeda; Mayra F Martínez-López; Michael Meyer; Edward J Migneco; Berna Nakanwagi; Karter B Neal; Winifred Neunzig; Máire Ní Leathlobhair; Sally J Nixon; Antonio Ortega-Pacheco; Francisco Pedraza-Ordoñez; Maria C Peleteiro; Katherine Polak; Ruth J Pye; John F Reece; Jose Rojas Gutierrez; Haleema Sadia; Sheila K Schmeling; Olga Shamanova; Alan G Sherlock; Maximilian Stammnitz; Audrey E Steenland-Smit; Alla Svitich; Lester J Tapia Martínez; Ismail Thoya Ngoka; Cristian G Torres; Elizabeth M Tudor; Mirjam G van der Wel; Bogdan A Viţălaru; Sevil A Vural; Oliver Walkinton; Jinhong Wang; Alvaro S Wehrle-Martinez; Sophie A E Widdowson; Michael R Stratton; Ludmil B Alexandrov; Iñigo Martincorena; Elizabeth P Murchison
Journal:  Science       Date:  2019-08-02       Impact factor: 47.728

5.  iMutSig: a web application to identify the most similar mutational signature using shiny.

Authors:  Zhi Yang; Priyatama Pandey; Paul Marjoram; Kimberly D Siegmund
Journal:  F1000Res       Date:  2020-06-10

6.  Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium.

Authors:  Manako Yamaguchi; Hirofumi Nakaoka; Kazuaki Suda; Kosuke Yoshihara; Tatsuya Ishiguro; Nozomi Yachida; Kyota Saito; Haruka Ueda; Kentaro Sugino; Yutaro Mori; Kaoru Yamawaki; Ryo Tamura; Sundaramoorthy Revathidevi; Teiichi Motoyama; Kazuki Tainaka; Roel G W Verhaak; Ituro Inoue; Takayuki Enomoto
Journal:  Nat Commun       Date:  2022-02-17       Impact factor: 14.919

7.  Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis.

Authors:  Shixiang Wang; Ziyu Tao; Tao Wu; Xue-Song Liu
Journal:  Bioinformatics       Date:  2021-07-12       Impact factor: 6.937

8.  The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils.

Authors:  Maximilian R Stammnitz; Tim H H Coorens; Kevin C Gori; Dane Hayes; Beiyuan Fu; Jinhong Wang; Daniel E Martin-Herranz; Ludmil B Alexandrov; Adrian Baez-Ortega; Syd Barthorpe; Alexandra Beck; Francesca Giordano; Graeme W Knowles; Young Mi Kwon; George Hall; Stacey Price; Ruth J Pye; Jose M C Tubio; Hannah V T Siddle; Sukhwinder Singh Sohal; Gregory M Woods; Ultan McDermott; Fengtang Yang; Mathew J Garnett; Zemin Ning; Elizabeth P Murchison
Journal:  Cancer Cell       Date:  2018-04-09       Impact factor: 38.585

9.  Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets.

Authors:  Jedidiah Carlson; Jun Z Li; Sebastian Zöllner
Journal:  BMC Genomics       Date:  2018-11-28       Impact factor: 3.969

10.  HiLDA: a statistical approach to investigate differences in mutational signatures.

Authors:  Zhi Yang; Priyatama Pandey; Darryl Shibata; David V Conti; Paul Marjoram; Kimberly D Siegmund
Journal:  PeerJ       Date:  2019-08-28       Impact factor: 2.984

  10 in total

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