Literature DB >> 34316057

Mutational signatures: emerging concepts, caveats and clinical applications.

Gene Koh1,2, Andrea Degasperi1,2, Xueqing Zou1,2, Sophie Momen1,2, Serena Nik-Zainal3,4.   

Abstract

Whole-genome sequencing has brought the cancer genomics community into new territory. Thanks to the sheer power provided by the thousands of mutations present in each patient's cancer, we have been able to discern generic patterns of mutations, termed 'mutational signatures', that arise during tumorigenesis. These mutational signatures provide new insights into the causes of individual cancers, revealing both endogenous and exogenous factors that have influenced cancer development. This Review brings readers up to date in a field that is expanding in computational, experimental and clinical directions. We focus on recent conceptual advances, underscoring some of the caveats associated with using the mutational signature frameworks and highlighting the latest experimental insights. We conclude by bringing attention to areas that are likely to see advancements in clinical applications.
© 2021. Springer Nature Limited.

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Year:  2021        PMID: 34316057     DOI: 10.1038/s41568-021-00377-7

Source DB:  PubMed          Journal:  Nat Rev Cancer        ISSN: 1474-175X            Impact factor:   60.716


  164 in total

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2.  Self-association of insulin and the role of hydrophobic bonding: a thermodynamic model of insulin dimerization.

Authors:  Y Pocker; S B Biswas
Journal:  Biochemistry       Date:  1981-07-21       Impact factor: 3.162

3.  Vibriocidal and agglutinating antibody patterns in cholera patients.

Authors:  R B Sack; D Barua; R Saxena; C C Carpenter
Journal:  J Infect Dis       Date:  1966-12       Impact factor: 5.226

Review 4.  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

5.  Oscillating heat flow from rabbit's pinna.

Authors:  F S Mohler; J E Heath
Journal:  Am J Physiol       Date:  1988-09

6.  Evolution of thyroid 127I stores measured by X-ray fluorescence in subacute thyroiditis.

Authors:  P Fragu; P Rougier; M Schlumberger; M Tubiana
Journal:  J Clin Endocrinol Metab       Date:  1982-01       Impact factor: 5.958

Review 7.  Mutational signatures: experimental design and analytical framework.

Authors:  Gene Koh; Xueqing Zou; Serena Nik-Zainal
Journal:  Genome Biol       Date:  2020-02-14       Impact factor: 13.583

8.  The mutational footprints of cancer therapies.

Authors:  Oriol Pich; Ferran Muiños; Martijn Paul Lolkema; Neeltje Steeghs; Abel Gonzalez-Perez; Nuria Lopez-Bigas
Journal:  Nat Genet       Date:  2019-11-18       Impact factor: 38.330

9.  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

10.  A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies.

Authors:  Andrea Degasperi; Tauanne Dias Amarante; Jan Czarnecki; Scott Shooter; Xueqing Zou; Dominik Glodzik; Sandro Morganella; Arjun S Nanda; Cherif Badja; Gene Koh; Sophie E Momen; Ilias Georgakopoulos-Soares; João M L Dias; Jamie Young; Yasin Memari; Helen Davies; Serena Nik-Zainal
Journal:  Nat Cancer       Date:  2020-02-17
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  31 in total

Review 1.  Therapeutic and prognostic insights from the analysis of cancer mutational signatures.

Authors:  Samuel W Brady; Alexander M Gout; Jinghui Zhang
Journal:  Trends Genet       Date:  2021-09-02       Impact factor: 11.639

Review 2.  Mapping the genomic diaspora of gastric cancer.

Authors:  Khay Guan Yeoh; Patrick Tan
Journal:  Nat Rev Cancer       Date:  2021-10-26       Impact factor: 60.716

Review 3.  Aristolochic acid-associated cancers: a public health risk in need of global action.

Authors:  Samrat Das; Shefali Thakur; Michael Korenjak; Viktoriya S Sidorenko; Felicia Fei-Lei Chung; Jiri Zavadil
Journal:  Nat Rev Cancer       Date:  2022-07-19       Impact factor: 69.800

4.  Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity.

Authors:  Xiaoxiao Ma; Nadeem Riaz; Robert M Samstein; Mark Lee; Vladimir Makarov; Cristina Valero; Diego Chowell; Fengshen Kuo; Douglas Hoen; Conall W R Fitzgerald; Hui Jiang; Jonathan Alektiar; Tyler J Alban; Ivan Juric; Prerana Bangalore Parthasarathy; Yu Zhao; Erich Y Sabio; Richa Verma; Raghvendra M Srivastava; Lynda Vuong; Wei Yang; Xiao Zhang; Jingming Wang; Lawrence K Chu; Stephen L Wang; Daniel W Kelly; Xin Pei; Jiapeng Chen; Rona Yaeger; Dmitriy Zamarin; Ahmet Zehir; Mithat Gönen; Luc G T Morris; Timothy A Chan
Journal:  Nat Genet       Date:  2022-07-11       Impact factor: 41.307

5.  Mutational Signatures Associate With Survival in Gastrointestinal Carcinomas.

Authors:  Peeter Karihtala; Katja Porvari; Outi Kilpivaara
Journal:  Cancer Genomics Proteomics       Date:  2022 Sep-Oct       Impact factor: 3.395

6.  Development of a versatile high-throughput mutagenesis assay with multiplexed short-read NGS using DNA-barcoded supF shuttle vector library amplified in E. coli.

Authors:  Hidehiko Kawai; Ren Iwata; Shungo Ebi; Ryusei Sugihara; Shogo Masuda; Chiho Fujiwara; Shingo Kimura; Hiroyuki Kamiya
Journal:  Elife       Date:  2022-10-10       Impact factor: 8.713

7.  A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand.

Authors:  Alina G Mikhailova; Alina A Mikhailova; Kristina Ushakova; Evgeny O Tretiakov; Dmitrii Iliushchenko; Victor Shamansky; Valeria Lobanova; Ivan Kozenkov; Bogdan Efimenko; Andrey A Yurchenko; Elena Kozenkova; Evgeny M Zdobnov; Vsevolod Makeev; Valerian Yurov; Masashi Tanaka; Irina Gostimskaya; Zoe Fleischmann; Sofia Annis; Melissa Franco; Kevin Wasko; Stepan Denisov; Wolfram S Kunz; Dmitry Knorre; Ilya Mazunin; Sergey Nikolaev; Jacques Fellay; Alexandre Reymond; Konstantin Khrapko; Konstantin Gunbin; Konstantin Popadin
Journal:  Nucleic Acids Res       Date:  2022-10-14       Impact factor: 19.160

8.  The impact of rare germline variants on human somatic mutation processes.

Authors:  Mischan Vali-Pour; Ben Lehner; Fran Supek
Journal:  Nat Commun       Date:  2022-06-28       Impact factor: 17.694

Review 9.  The Dynamics of Somatic Mutagenesis During Life in Humans.

Authors:  Freek Manders; Ruben van Boxtel; Sjors Middelkamp
Journal:  Front Aging       Date:  2021-12-17

10.  Signatures of copy number alterations in human cancer.

Authors:  Ludmil B Alexandrov; Nischalan Pillay; Christopher D Steele; Ammal Abbasi; S M Ashiqul Islam; Amy L Bowes; Azhar Khandekar; Kerstin Haase; Shadi Hames-Fathi; Dolapo Ajayi; Annelien Verfaillie; Pawan Dhami; Alex McLatchie; Matt Lechner; Nicholas Light; Adam Shlien; David Malkin; Andrew Feber; Paula Proszek; Tom Lesluyes; Fredrik Mertens; Adrienne M Flanagan; Maxime Tarabichi; Peter Van Loo
Journal:  Nature       Date:  2022-06-15       Impact factor: 69.504

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