Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
18 05 2022
18 05 2022
Historique:
received:
17
09
2021
accepted:
21
04
2022
entrez:
18
5
2022
pubmed:
19
5
2022
medline:
21
5
2022
Statut:
epublish
Résumé
The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology.
Identifiants
pubmed: 35585047
doi: 10.1038/s41467-022-30233-7
pii: 10.1038/s41467-022-30233-7
pmc: PMC9117241
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2485Subventions
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Informations de copyright
© 2022. The Author(s).
Références
Nat Genet. 2018 Aug;50(8):1189-1195
pubmed: 30013179
Nat Commun. 2021 Jan 21;12(1):498
pubmed: 33479225
Mod Pathol. 2019 Jun;32(6):764-773
pubmed: 30723300
Science. 2018 Dec 7;362(6419):1165-1170
pubmed: 30523111
Nature. 2013 Jul 11;499(7457):214-218
pubmed: 23770567
Cell. 2014 Oct 23;159(3):676-90
pubmed: 25417114
Nucleic Acids Res. 2016 Sep 19;44(16):e131
pubmed: 27270079
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Hum Mutat. 2018 Nov;39(11):1542-1552
pubmed: 30311369
Nat Biotechnol. 2013 Nov;31(11):1023-31
pubmed: 24142049
Nat Commun. 2021 May 28;12(1):3230
pubmed: 34050156
Genome Biol. 2019 Oct 21;20(1):213
pubmed: 31639029
JCO Precis Oncol. 2018;2018:
pubmed: 30027144
Curr Protoc Bioinformatics. 2016 Dec 8;56:15.10.1-15.10.18
pubmed: 27930805
Nat Biotechnol. 2019 Nov;37(11):1351-1360
pubmed: 31570899
Cancer Discov. 2021 Nov;11(11):2780-2795
pubmed: 34112699
Front Oncol. 2019 Aug 06;9:713
pubmed: 31448229
Acta Neuropathol. 2019 May;137(5):851-854
pubmed: 30877433
Lancet Oncol. 2020 Oct;21(10):1353-1365
pubmed: 32919526
Nat Commun. 2020 Feb 5;11(1):733
pubmed: 32024817
Genome Res. 2021 Mar;31(3):448-460
pubmed: 33441414
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Cancer Biol Ther. 2017 Jul 3;18(7):519-533
pubmed: 28494185
Cell Rep. 2014 Apr 10;7(1):104-12
pubmed: 24703847
Cancer Discov. 2021 Dec 1;11(12):3008-3027
pubmed: 34301788
Nat Commun. 2020 Jul 17;11(1):3617
pubmed: 32680998
Nature. 2020 May;581(7809):434-443
pubmed: 32461654
N Engl J Med. 2012 Mar 8;366(10):883-892
pubmed: 22397650
Cancer Cell. 2015 Feb 9;27(2):298-311
pubmed: 25670083
BMC Bioinformatics. 2020 Nov 30;21(1):549
pubmed: 33256603
Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8
pubmed: 26582918
Nat Med. 2017 Jun;23(6):703-713
pubmed: 28481359
Nat Commun. 2018 Sep 27;9(1):3962
pubmed: 30262806
Genome Biol. 2020 Sep 7;21(1):239
pubmed: 32894187
Nat Commun. 2021 Feb 24;12(1):1269
pubmed: 33627664
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Genet Med. 2018 Oct;20(10):1196-1205
pubmed: 29388947
Nat Genet. 2015 Dec;47(12):1411-4
pubmed: 26523776
Bioinformatics. 2016 Oct 15;32(20):3196-3198
pubmed: 27354699
Bioinformatics. 2018 Mar 1;34(5):867-868
pubmed: 29096012
Nucleic Acids Res. 2014 May;42(9):e75
pubmed: 24609383
Nature. 2018 Mar 22;555(7697):469-474
pubmed: 29539639
N Engl J Med. 2018 Feb 22;378(8):731-739
pubmed: 29466156
Genet Med. 2015 May;17(5):405-24
pubmed: 25741868
Cell. 2011 Jan 7;144(1):27-40
pubmed: 21215367
Nature. 2020 Feb;578(7793):94-101
pubmed: 32025018
J Mol Diagn. 2021 Jul;23(7):816-833
pubmed: 33964451
Am J Transplant. 2012 Jul;12(7):1908-17
pubmed: 22420456
Sci Transl Med. 2014 Feb 19;6(224):224ra24
pubmed: 24553385
Genome Res. 2017 Dec;27(12):2050-2060
pubmed: 29097403
Nat Rev Genet. 2021 Aug;22(8):483-501
pubmed: 33762738
Oncotarget. 2015 Apr 10;6(10):7493-503
pubmed: 25595889
BMC Cancer. 2019 Mar 14;19(1):232
pubmed: 30871494
Cell. 2019 May 2;177(4):821-836.e16
pubmed: 30982602
Nucleic Acids Res. 2017 Jan 4;45(D1):D777-D783
pubmed: 27899578
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
PLoS One. 2021 Jan 20;16(1):e0245582
pubmed: 33471860
Oncotarget. 2018 Jan 30;9(21):15792-15815
pubmed: 29644010
Genome Med. 2018 Apr 25;10(1):33
pubmed: 29695279
Nat Med. 2020 Nov;26(11):1742-1753
pubmed: 33020650
Cancer Res. 2020 Jun 15;80(12):2663-2675
pubmed: 32291317
Nat Genet. 2016 Nov;48(11):1339-1348
pubmed: 27723760
Cancer. 2006 Sep 15;107(6):1391-9
pubmed: 16917952
Nature. 2018 Mar 15;555(7696):321-327
pubmed: 29489754
Mol Aspects Med. 2020 Apr;72:100819
pubmed: 31563277
Bioinformatics. 2009 Nov 1;25(21):2865-71
pubmed: 19561018
JAMA Oncol. 2016 May 01;2(5):616-624
pubmed: 26822237
N Engl J Med. 2021 Mar 11;384(10):924-935
pubmed: 33704937
Nat Methods. 2018 Aug;15(8):591-594
pubmed: 30013048
Nat Genet. 2019 Dec;51(12):1732-1740
pubmed: 31740835
BMC Genomics. 2018 Nov 1;19(1):786
pubmed: 30382840
Nat Rev Dis Primers. 2019 Jan 7;5(1):1
pubmed: 30617281
Cell. 2017 Nov 16;171(5):1042-1056.e10
pubmed: 29056344
J Mol Diagn. 2018 Nov;20(6):822-835
pubmed: 30138725
Genome Res. 2018 Apr;28(4):581-591
pubmed: 29535149
Nat Genet. 2016 Mar;48(3):265-72
pubmed: 26829750
N Engl J Med. 2019 Nov 28;381(22):2145-2156
pubmed: 31774959
Nat Cancer. 2021 Mar;2:357-365
pubmed: 34308366
Bioinformatics. 2014 Apr 1;30(7):1015-6
pubmed: 24371154
Clin Cancer Res. 2019 Aug 1;25(15):4712-4722
pubmed: 31028088
Cell. 2012 May 25;149(5):994-1007
pubmed: 22608083
Curr Protoc Bioinformatics. 2015 Dec 17;52:15.8.1-15.8.11
pubmed: 26678383
Cancer Treat Rev. 2014 Dec;40(10):1153-60
pubmed: 25455730
Ann Oncol. 2017 Dec 01;28(12):3076-3082
pubmed: 28950321
J Mol Diagn. 2015 May;17(3):251-64
pubmed: 25801821
Nat Med. 2017 Apr;23(4):517-525
pubmed: 28288110