Identification of combinations of somatic mutations that predict cancer survival and immunotherapy benefit.
Journal
NAR cancer
ISSN: 2632-8674
Titre abrégé: NAR Cancer
Pays: England
ID NLM: 101769553
Informations de publication
Date de publication:
Jun 2021
Jun 2021
Historique:
received:
01
02
2021
revised:
18
04
2021
accepted:
28
04
2021
entrez:
24
5
2021
pubmed:
25
5
2021
medline:
25
5
2021
Statut:
epublish
Résumé
Cancer evolves through the accumulation of somatic mutations over time. Although several methods have been developed to characterize mutational processes in cancers, these have not been specifically designed to identify mutational patterns that predict patient prognosis. Here we present CLICnet, a method that utilizes mutational data to cluster patients by survival rate. CLICnet employs Restricted Boltzmann Machines, a type of generative neural network, which allows for the capture of complex mutational patterns associated with patient survival in different cancer types. For some cancer types, clustering produced by CLICnet also predicts benefit from anti-PD1 immune checkpoint blockade therapy, whereas for other cancer types, the mutational processes associated with survival are different from those associated with the improved anti-PD1 survival benefit. Thus, CLICnet has the ability to systematically identify and catalogue combinations of mutations that predict cancer survival, unveiling intricate associations between mutations, survival, and immunotherapy benefit.
Identifiants
pubmed: 34027407
doi: 10.1093/narcan/zcab017
pii: zcab017
pmc: PMC8127965
doi:
Types de publication
Journal Article
Langues
eng
Pagination
zcab017Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of NAR Cancer.
Références
Nature. 2013 Jul 11;499(7457):214-218
pubmed: 23770567
Gastroenterology. 2010 Jun;138(6):2073-2087.e3
pubmed: 20420947
Ann Oncol. 2019 Jan 1;30(1):44-56
pubmed: 30395155
PLoS Comput Biol. 2013;9(5):e1003054
pubmed: 23717195
J Clin Oncol. 2019 Oct 1;37(28):2518-2527
pubmed: 31154919
Nat Commun. 2017 Oct 11;8(1):857
pubmed: 29021619
N Engl J Med. 2004 Dec 30;351(27):2817-26
pubmed: 15591335
Nat Genet. 2014 May;46(5):487-91
pubmed: 24728294
Nat Methods. 2013 Nov;10(11):1108-15
pubmed: 24037242
Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947
pubmed: 30371878
Cell Rep. 2016 Mar 15;14(10):2476-89
pubmed: 26947078
Cell. 2017 Nov 2;171(4):934-949.e16
pubmed: 29033130
Clin Cancer Res. 2016 Feb 15;22(4):813-20
pubmed: 26880610
Clin Cancer Res. 2016 Sep 15;22(18):4585-93
pubmed: 27225694
Nucleic Acids Res. 2015 Jan;43(Database issue):D805-11
pubmed: 25355519
Nat Genet. 2015 Feb;47(2):106-14
pubmed: 25501392
Science. 2015 Apr 3;348(6230):124-8
pubmed: 25765070
Nat Rev Genet. 2012 Nov;13(11):795-806
pubmed: 23044827
Cell. 2011 Mar 4;144(5):646-74
pubmed: 21376230
Cell. 2018 Apr 5;173(2):371-385.e18
pubmed: 29625053
Chest. 2004 Jan;125(1):27-37
pubmed: 14718417
Front Genet. 2019 Apr 10;10:265
pubmed: 31024613
Elife. 2018 Dec 11;7:
pubmed: 30526857
Genome Med. 2020 Mar 30;12(1):33
pubmed: 32228719
J Natl Cancer Inst. 2013 Jan 16;105(2):141-8
pubmed: 23257159
Gastroenterology. 1994 Jan;106(1):42-8
pubmed: 8276207
Nature. 2013 Sep 19;501(7467):338-45
pubmed: 24048066
PLoS Comput Biol. 2019 Mar 28;15(3):e1006658
pubmed: 30921324
Br J Cancer. 2013 Apr 30;108(8):1757-64
pubmed: 23511557
N Engl J Med. 2015 Jun 25;372(26):2509-20
pubmed: 26028255
Nat Genet. 2018 Sep;50(9):1271-1281
pubmed: 30150660
Cell Rep. 2013 Jan 31;3(1):246-59
pubmed: 23318258
Nat Med. 2019 Dec;25(12):1916-1927
pubmed: 31792460
J Clin Oncol. 2015 Jun 10;33(17):1974-82
pubmed: 25605845
J Clin Oncol. 2010 Jan 10;28(2):222-31
pubmed: 19996031
Eur Urol. 2015 Jul;68(1):123-31
pubmed: 25465337
Genome Biol. 2008 Oct 13;9(10):R150
pubmed: 18851746
Nat Med. 2019 Feb;25(2):221-224
pubmed: 30510256
Oncoimmunology. 2018 Dec 24;8(3):1550341
pubmed: 30723579
Nat Med. 2017 Jun;23(6):703-713
pubmed: 28481359
Thorac Cancer. 2018 Apr;9(4):423-430
pubmed: 29488330
Science. 2016 Nov 4;354(6312):618-622
pubmed: 27811275
Nat Genet. 2016 Jun;48(6):607-16
pubmed: 27158780
Nat Commun. 2017 Dec 19;8(1):2193
pubmed: 29259186
Eur J Cancer. 2016 Jun;60:210-25
pubmed: 27084345
Pac Symp Biocomput. 2012;:55-66
pubmed: 22174262
Cancer. 2005 Jun 25;105(3):165-70
pubmed: 15822120
Cancer Discov. 2018 Sep;8(9):1069-1086
pubmed: 30115704
Carcinogenesis. 2000 Mar;21(3):379-85
pubmed: 10688858
Genome Res. 2012 Feb;22(2):375-85
pubmed: 21653252
J Natl Cancer Inst. 2007 Jun 20;99(12):929-35
pubmed: 17565157
Nat Genet. 2018 Sep;50(9):1262-1270
pubmed: 30104763
Nucleic Acids Res. 2018 Jan 4;46(D1):D964-D970
pubmed: 29145625
Cell Rep. 2018 Apr 3;23(1):313-326.e5
pubmed: 29617669
Int J Cancer. 2007 Oct 15;121(8):1771-8
pubmed: 17590872
Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50
pubmed: 20952405
Nature. 2020 Feb;578(7793):94-101
pubmed: 32025018
N Engl J Med. 2015 Oct 22;373(17):1627-39
pubmed: 26412456
Nat Rev Cancer. 2020 Jan;20(1):42-56
pubmed: 31819232
Nat Methods. 2005 Apr;2(4):285-90
pubmed: 15782221
Cancer Discov. 2012 May;2(5):401-4
pubmed: 22588877
Eur J Cancer. 2016 Jun;60:190-209
pubmed: 27085692
Nat Commun. 2014 Dec 22;5:5893
pubmed: 25531467
Science. 2006 Jul 28;313(5786):504-7
pubmed: 16873662
Cell. 2018 Apr 5;173(2):400-416.e11
pubmed: 29625055
Clin Cancer Res. 2017 Aug 1;23(15):4077-4085
pubmed: 28280090
Nat Genet. 2013 Oct;45(10):1113-20
pubmed: 24071849
Sci Rep. 2013 Oct 02;3:2652
pubmed: 24084870
Chin Med J (Engl). 2016 Feb 20;129(4):448-55
pubmed: 26879019
Oncogene. 2018 Jul;37(29):3924-3936
pubmed: 29695832
Nat Rev Drug Discov. 2018 Mar;17(3):183-196
pubmed: 29217837
Cell. 2018 Apr 5;173(2):291-304.e6
pubmed: 29625048
Nature. 2013 Aug 22;500(7463):415-21
pubmed: 23945592
Sci Signal. 2013 Apr 02;6(269):pl1
pubmed: 23550210
Eur Urol. 2014 Sep;66(3):550-60
pubmed: 24836057
Genome Res. 2017 Sep;27(9):1573-1588
pubmed: 28768687
J Clin Oncol. 2015 Jan 1;33(1):42-50
pubmed: 25332244
Nucleic Acids Res. 2015 Jan;43(Database issue):D812-7
pubmed: 25392408
Genome Biol. 2008;9(6):229
pubmed: 18598372
Breast Cancer Res. 2004;6(1):R8-R17
pubmed: 14680495
Nat Genet. 2019 Feb;51(2):202-206
pubmed: 30643254
Nat Med. 2016 Nov;22(11):1342-1350
pubmed: 27694933
Sci Transl Med. 2018 Sep 19;10(459):
pubmed: 30232229
Cancer Prev Res (Phila). 2011 Jul;4(7):1002-10
pubmed: 21733824
Nature. 2013 Sep 19;501(7467):328-37
pubmed: 24048065
Nat Rev Cancer. 2007 Oct;7(10):778-90
pubmed: 17882278
J Mol Diagn. 2015 May;17(3):251-64
pubmed: 25801821