Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers.
Journal
Science advances
ISSN: 2375-2548
Titre abrégé: Sci Adv
Pays: United States
ID NLM: 101653440
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
21
11
2019
accepted:
10
06
2020
entrez:
25
8
2020
pubmed:
25
8
2020
medline:
12
4
2022
Statut:
epublish
Résumé
Interpreting the function of noncoding mutations in cancer genomes remains a major challenge. Here, we developed a computational framework to identify putative causal noncoding mutations of all classes by joint analysis of mutation and gene expression data. We identified thousands of SNVs/small indels and structural variants as putative causal mutations in five major pediatric cancers. We experimentally validated the oncogenic role of
Identifiants
pubmed: 32832663
doi: 10.1126/sciadv.aba3064
pii: aba3064
pmc: PMC7439310
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
eaba3064Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM104369
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM108716
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA226187
Pays : United States
Organisme : NCI NIH HHS
ID : U2C CA233285
Pays : United States
Organisme : NCI NIH HHS
ID : K08 CA184418
Pays : United States
Informations de copyright
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).
Références
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
Nat Biotechnol. 2016 Feb;34(2):184-191
pubmed: 26780180
Nat Biotechnol. 2014 Mar;32(3):246-51
pubmed: 24531798
Cell. 2013 Nov 7;155(4):934-47
pubmed: 24119843
Nature. 2018 Oct;562(7727):373-379
pubmed: 30209392
Br J Haematol. 2017 Mar;176(6):867-882
pubmed: 27984637
Nucleic Acids Res. 2016 Jan 4;44(D1):D164-71
pubmed: 26438538
Leukemia. 2011 Nov;25(11):1704-10
pubmed: 21647152
Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):7356-7361
pubmed: 29941555
Nature. 2015 Oct 29;526(7575):700-4
pubmed: 26466568
Nat Genet. 2016 Mar;48(3):265-72
pubmed: 26829750
Haematologica. 2018 Apr;103(4):614-625
pubmed: 29326122
Genome Biol. 2015 Aug 08;16:160
pubmed: 26253137
Curr Opin Genet Dev. 2014 Apr;25:93-100
pubmed: 24598232
Cell Cycle. 2005 Dec;4(12):1842-6
pubmed: 16294040
Crit Rev Oncog. 2011;16(1-2):13-24
pubmed: 22150304
Nat Genet. 2018 Apr;50(4):613-620
pubmed: 29610481
PLoS One. 2014 May 06;9(5):e96636
pubmed: 24800817
BMC Cancer. 2018 Apr 23;18(1):458
pubmed: 29688850
Leuk Res. 2017 May;56:7-12
pubmed: 28152414
Nat Genet. 2013 Mar;45(3):279-84
pubmed: 23334666
Nucleic Acids Res. 2016 Jan 4;44(D1):D959-68
pubmed: 26519468
PLoS One. 2015 Aug 25;10(8):e0134706
pubmed: 26305332
Proc Natl Acad Sci U S A. 2014 May 27;111(21):E2191-9
pubmed: 24821768
Genome Res. 2017 Feb;27(2):185-195
pubmed: 27903646
Leukemia. 2013 Mar;27(3):578-85
pubmed: 23044487
Eur J Pharmacol. 2018 Feb 5;820:113-129
pubmed: 29242118
Proc Natl Acad Sci U S A. 2018 Feb 6;115(6):E1229-E1238
pubmed: 29374092
Nat Methods. 2006 Nov;3(11):917-22
pubmed: 17124735
Mod Pathol. 2010 Sep;23(9):1261-8
pubmed: 20581805
Cell. 2014 Sep 11;158(6):1431-1443
pubmed: 25215497
Nature. 2010 Apr 15;464(7291):993-8
pubmed: 20393554
Nature. 2018 Mar 15;555(7696):371-376
pubmed: 29489755
Immunol Rev. 2014 Sep;261(1):126-40
pubmed: 25123281
Curr Opin Genet Dev. 2020 Feb;60:56-62
pubmed: 32163830
Bioinformatics. 2010 Jul 1;26(13):1579-86
pubmed: 20453004
Nat Cell Biol. 2013 Apr;15(4):363-72
pubmed: 23524953
Cell. 2013 May 9;153(4):919-29
pubmed: 23663786
Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5564-73
pubmed: 25512523
Amino Acids. 2013 Jan;44(1):161-77
pubmed: 21984379
Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44
pubmed: 19966280
Nat Methods. 2014 Aug;11(8):783-784
pubmed: 25075903
Nat Commun. 2014 Sep 10;5:4846
pubmed: 25204415
Nat Genet. 2016 Dec;48(12):1551-1556
pubmed: 27798625
Cell. 2014 Apr 10;157(2):369-381
pubmed: 24703711
Nature. 2018 Mar 15;555(7696):321-327
pubmed: 29489754
Cancer Discov. 2015 Oct;5(10):1058-71
pubmed: 26229090
BMC Bioinformatics. 2008 Dec 10;9:530
pubmed: 19077204
Nature. 2014 Jul 24;511(7510):428-34
pubmed: 25043047
PLoS One. 2016 Jul 08;11(7):e0158761
pubmed: 27391105
Nature. 2015 Dec 17;528(7582):418-21
pubmed: 26560027
Science. 2014 Dec 12;346(6215):1373-7
pubmed: 25394790
Nat Commun. 2014 Jun 03;5:3964
pubmed: 24888982
Cell Death Dis. 2017 Mar 23;8(3):e2700
pubmed: 28333143
Blood. 2015 Sep 17;126(12):1462-72
pubmed: 26265695
N Engl J Med. 2014 Sep 11;371(11):1005-15
pubmed: 25207766