Beyond the Variants: Mutational Patterns in Next-Generation Sequencing Data for Cancer Precision Medicine.
homologous recombination deficiency
microsatellite instability
mutational pattern
mutational signature
tumor mutational burden
Journal
Frontiers in cell and developmental biology
ISSN: 2296-634X
Titre abrégé: Front Cell Dev Biol
Pays: Switzerland
ID NLM: 101630250
Informations de publication
Date de publication:
2020
2020
Historique:
received:
23
11
2019
accepted:
24
04
2020
entrez:
9
6
2020
pubmed:
9
6
2020
medline:
9
6
2020
Statut:
epublish
Résumé
Massively parallel sequencing, also referred to as "next-generation sequencing" (NGS) provides not only information about simple, single nucleotide alterations, but it can also provide information on complex variations, such as insertions and deletions, copy number alterations, and structural variants. In addition to identifying individual alterations, genome-wide biomarkers can be discerned from somatic cancer NGS data, broadly termed mutational patterns and signatures. This review will focus on several of the most common genome-wide biomarkers such as tumor mutational burden, microsatellite instability, homologous recombination deficiency, and mutational signatures.
Identifiants
pubmed: 32509788
doi: 10.3389/fcell.2020.00370
pmc: PMC7248322
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
370Informations de copyright
Copyright © 2020 Parilla and Ritterhouse.
Références
Nature. 2013 Jul 11;499(7457):214-218
pubmed: 23770567
Cancer Res. 1998 Nov 15;58(22):5248-57
pubmed: 9823339
NPJ Breast Cancer. 2018 Jul 2;4:16
pubmed: 29978035
N Engl J Med. 2012 Jun 28;366(26):2443-54
pubmed: 22658127
Genome Med. 2017 Apr 19;9(1):34
pubmed: 28420421
PLoS Comput Biol. 2016 Apr 21;12(4):e1004873
pubmed: 27100738
J Biol Chem. 2018 Jul 6;293(27):10524-10535
pubmed: 29599286
Cancer Discov. 2012 Apr;2(4):366-375
pubmed: 22576213
Nature. 2013 Aug 22;500(7463):415-21
pubmed: 23945592
Nature. 2008 Feb 28;451(7182):1116-20
pubmed: 18264087
J Natl Cancer Inst. 2018 Jul 1;110(7):704-713
pubmed: 29788099
Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947
pubmed: 30371878
Lancet Oncol. 2017 Jan;18(1):31-41
pubmed: 27932067
Arch Pathol Lab Med. 2017 Dec;141(12):1679-1685
pubmed: 29028368
Science. 2015 Apr 3;348(6230):124-8
pubmed: 25765070
Lancet. 2017 Oct 28;390(10106):1949-1961
pubmed: 28916367
N Engl J Med. 2012 Jun 28;366(26):2455-65
pubmed: 22658128
Front Oncol. 2018 Dec 12;8:621
pubmed: 30631754
Semin Oncol. 2019 Jun;46(3):261-270
pubmed: 31537299
Ann Oncol. 2011 Dec;22(12):2616-24
pubmed: 22071650
Soc Sci Med. 1989;28(4):347-54
pubmed: 2705007
N Engl J Med. 2015 Jun 25;372(26):2509-20
pubmed: 26028255
Cancer Res. 2012 Nov 1;72(21):5454-62
pubmed: 22933060
Clin Cancer Res. 2016 Aug 1;22(15):3764-73
pubmed: 26957554
Breast Cancer Res. 2014 Dec 05;16(6):475
pubmed: 25475740
Clin Cancer Res. 2014 Oct 1;20(19):5064-74
pubmed: 24714771
Nature. 2005 Apr 14;434(7035):917-21
pubmed: 15829967
Transl Lung Cancer Res. 2018 Dec;7(6):703-715
pubmed: 30505715
Nat Med. 2018 May;24(5):628-637
pubmed: 29713086
Nat Med. 2017 Jun;23(6):703-713
pubmed: 28481359
Br J Cancer. 2012 Nov 6;107(10):1776-82
pubmed: 23047548
Int J Cancer. 2019 Feb 15;144(4):848-858
pubmed: 30238975
Int J Cancer. 2019 May 1;144(9):2303-2312
pubmed: 30446996
Nat Rev Mol Cell Biol. 2017 Aug;18(8):495-506
pubmed: 28512351
N Engl J Med. 2016 Nov 10;375(19):1823-1833
pubmed: 27718847
Clin Cancer Res. 2017 Dec 15;23(24):7521-7530
pubmed: 29246904
Nature. 2005 Apr 14;434(7035):913-7
pubmed: 15829966
Genes Chromosomes Cancer. 2019 Aug;58(8):578-588
pubmed: 30664300
Nature. 2020 Feb;578(7793):94-101
pubmed: 32025018
N Engl J Med. 2019 Oct 17;381(16):1535-1546
pubmed: 31562797
BMC Genomics. 2017 Jan 5;18(1):16
pubmed: 28056804
Ann Oncol. 2018 Oct 1;29(Suppl 4):iv192-iv237
pubmed: 30285222
Cancer Discov. 2017 Sep;7(9):984-998
pubmed: 28588062
J Mol Diagn. 2017 Jan;19(1):57-64
pubmed: 27810331
JCI Insight. 2016 Nov 17;1(19):e87062
pubmed: 27882345
Fam Cancer. 2017 Jul;16(3):377-387
pubmed: 28176204
Clin Cancer Res. 2019 Jul 1;25(13):3753-3758
pubmed: 30787022
Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7
pubmed: 271968
Nature. 2008 Feb 28;451(7182):1111-5
pubmed: 18264088
Cancer Discov. 2017 Sep;7(9):1006-1017
pubmed: 28450425
Theranostics. 2017 Aug 22;7(14):3585-3594
pubmed: 28912897
Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17079-84
pubmed: 18971340
N Engl J Med. 2017 Oct 12;377(15):1409-1412
pubmed: 29020592
Nature. 2011 Feb 10;470(7333):198-203
pubmed: 21307932
J Clin Oncol. 2019 Oct 1;37(28):2518-2527
pubmed: 31154919
Bioinformatics. 2014 Oct;30(19):2813-5
pubmed: 24907369
Nat Rev Genet. 2014 Sep;15(9):585-98
pubmed: 24981601
Science. 2017 Jul 28;357(6349):409-413
pubmed: 28596308
Nat Med. 2016 Nov;22(11):1342-1350
pubmed: 27694933
Nat Commun. 2017 May 03;8:14755
pubmed: 28466842
Nat Med. 2017 Apr;23(4):517-525
pubmed: 28288110