NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology.
Journal
NPJ precision oncology
ISSN: 2397-768X
Titre abrégé: NPJ Precis Oncol
Pays: England
ID NLM: 101708166
Informations de publication
Date de publication:
26 Oct 2023
26 Oct 2023
Historique:
received:
02
04
2023
accepted:
26
09
2023
medline:
27
10
2023
pubmed:
27
10
2023
entrez:
26
10
2023
Statut:
epublish
Résumé
Analysis of selected cancer genes has become an important tool in precision oncology but cannot fully capture the molecular features and, most importantly, vulnerabilities of individual tumors. Observational and interventional studies have shown that decision-making based on comprehensive molecular characterization adds significant clinical value. However, the complexity and heterogeneity of the resulting data are major challenges for disciplines involved in interpretation and recommendations for individualized care, and limited information exists on how to approach multilayered tumor profiles in clinical routine. We report our experience with the practical use of data from whole-genome or exome and RNA sequencing and DNA methylation profiling within the MASTER (Molecularly Aided Stratification for Tumor Eradication Research) program of the National Center for Tumor Diseases (NCT) Heidelberg and Dresden and the German Cancer Research Center (DKFZ). We cover all relevant steps of an end-to-end precision oncology workflow, from sample collection, molecular analysis, and variant prioritization to assigning treatment recommendations and discussion in the molecular tumor board. To provide insight into our approach to multidimensional tumor profiles and guidance on interpreting their biological impact and diagnostic and therapeutic implications, we present case studies from the NCT/DKFZ molecular tumor board that illustrate our daily practice. This manual is intended to be useful for physicians, biologists, and bioinformaticians involved in the clinical interpretation of genome-wide molecular information.
Identifiants
pubmed: 37884744
doi: 10.1038/s41698-023-00458-w
pii: 10.1038/s41698-023-00458-w
pmc: PMC10603123
doi:
Types de publication
Journal Article
Langues
eng
Pagination
109Informations de copyright
© 2023. The Author(s).
Références
Oncologist. 2014 Jun;19(6):631-6
pubmed: 24797821
iScience. 2018 Oct 26;8:49-53
pubmed: 30273912
Eur J Cancer. 2011 Nov;47(17):2493-511
pubmed: 22033323
Ann Surg Oncol. 2015 Dec;22(13):4287-94
pubmed: 25971960
Lancet Oncol. 2019 Oct;20(10):1454-1466
pubmed: 31405822
Oncotarget. 2015 Dec 15;6(40):42429-44
pubmed: 26643872
JCO Precis Oncol. 2017;2017:
pubmed: 30003184
Lancet Oncol. 2019 Sep;20(9):1295-1305
pubmed: 31351869
Nat Commun. 2019 Apr 9;10(1):1635
pubmed: 30967556
JCO Precis Oncol. 2020 Nov;4:757-766
pubmed: 35050752
Nucleic Acids Res. 2019 Jan 8;47(D1):D941-D947
pubmed: 30371878
Hum Mutat. 2014 Mar;35(3):384-91
pubmed: 24282159
J Biotechnol. 2017 Nov 10;261:53-62
pubmed: 28803971
Genome Med. 2020 Jan 14;12(1):8
pubmed: 31937368
Nat Med. 2019 May;25(5):767-775
pubmed: 31011208
Cancer Discov. 2021 Nov;11(11):2780-2795
pubmed: 34112699
JCO Precis Oncol. 2018 Aug 16;2:
pubmed: 32913998
Nat Med. 2019 May;25(5):711-712
pubmed: 31036881
Cancer Res. 2012 Nov 1;72(21):5454-62
pubmed: 22933060
Genome Res. 2021 Mar;31(3):448-460
pubmed: 33441414
J Cancer Res Clin Oncol. 2023 May;149(5):1905-1915
pubmed: 35796778
JCO Precis Oncol. 2017 Jul;2017:
pubmed: 28890946
N Engl J Med. 2015 Jun 4;372(23):2235-42
pubmed: 26014595
Nucleic Acids Res. 2020 Jan 8;48(D1):D835-D844
pubmed: 31777943
JCO Precis Oncol. 2021 Apr 22;5:
pubmed: 34036222
Br J Cancer. 2012 Nov 6;107(10):1776-82
pubmed: 23047548
J Clin Oncol. 2005 Apr 1;23(10):2272-9
pubmed: 15800318
Nat Commun. 2021 Jan 21;12(1):498
pubmed: 33479225
Nature. 2022 Jun;606(7916):984-991
pubmed: 35705804
Ann Oncol. 2022 Nov;33(11):1186-1199
pubmed: 35988656
Genes Chromosomes Cancer. 2022 Jun;61(6):303-313
pubmed: 34331337
Nature. 2022 Jun;606(7916):976-983
pubmed: 35705807
Ann Oncol. 2020 Nov;31(11):1491-1505
pubmed: 32853681
Cell Rep Med. 2020 Oct 20;1(7):100128
pubmed: 33205077
Sci Transl Med. 2015 Apr 15;7(283):283ra53
pubmed: 25877891
JCO Clin Cancer Inform. 2023 Mar;7:e2200147
pubmed: 36888935
Nature. 2018 Mar 22;555(7697):469-474
pubmed: 29539639
Genet Med. 2022 May;24(5):986-998
pubmed: 35101336
Front Oncol. 2021 Jun 11;11:678966
pubmed: 34178665
Genet Med. 2015 May;17(5):405-24
pubmed: 25741868
Genome Biol. 2019 Sep 10;20(1):195
pubmed: 31506093
Cancer Discov. 2017 Oct;7(10):1116-1135
pubmed: 28667006
Brief Bioinform. 2021 Nov 5;22(6):
pubmed: 33971666
Trends Cancer. 2020 Sep;6(9):738-744
pubmed: 32517959
Cancer Discov. 2012 May;2(5):401-4
pubmed: 22588877
Int J Cancer. 2021 Mar 15;148(6):1438-1451
pubmed: 32949162
Genes Chromosomes Cancer. 2021 May;60(5):314-331
pubmed: 33222322
Cell. 2018 Apr 5;173(2):355-370.e14
pubmed: 29625052
N Engl J Med. 2019 Jul 25;381(4):317-327
pubmed: 31157963
J Mol Diagn. 2017 Jan;19(1):4-23
pubmed: 27993330
Nat Commun. 2018 Jan 2;9(1):20
pubmed: 29295995
JCO Precis Oncol. 2018 Nov;2:1-13
pubmed: 35135162
JAMA Oncol. 2016 May 01;2(5):616-624
pubmed: 26822237
BMC Bioinformatics. 2019 May 28;20(1):272
pubmed: 31138115
JCO Precis Oncol. 2019 Dec;3:1-8
pubmed: 35100714
Genome Med. 2019 Nov 29;11(1):76
pubmed: 31779674
ESMO Open. 2021 Dec;6(6):100310
pubmed: 34808524
Nat Commun. 2017 Oct 30;8(1):1197
pubmed: 29084941
Nature. 2013 Aug 22;500(7463):415-21
pubmed: 23945592
Annu Rev Genomics Hum Genet. 2019 Aug 31;20:413-432
pubmed: 30995147
Hum Genomics. 2016 Jan 16;10:4
pubmed: 26772741
Nat Commun. 2022 Aug 2;13(1):4485
pubmed: 35918329
Sci Signal. 2013 Apr 02;6(269):pl1
pubmed: 23550210
Cancer Discov. 2018 Sep;8(9):1087-1095
pubmed: 29802158
J Clin Oncol. 2013 Sep 10;31(26):3182-90
pubmed: 23775962
Oral Oncol. 2016 Jul;58:41-8
pubmed: 27311401
Bioinformatics. 2014 Apr 1;30(7):1015-6
pubmed: 24371154
Cancer Cell. 2018 Jun 11;33(6):1128-1141.e7
pubmed: 29861296
Int J Cancer. 2017 Sep 1;141(5):877-886
pubmed: 28597939
Bioinformatics. 2019 Jun 1;35(11):1978-1980
pubmed: 30376034
Int J Cancer. 2019 Dec 1;145(11):2996-3010
pubmed: 31008532
Cancer Discov. 2018 Feb;8(2):174-183
pubmed: 29247016
Nat Commun. 2018 Jan 10;9(1):144
pubmed: 29321523
Cancer Res. 2016 Nov 1;76(21):6140-6142
pubmed: 27803101
Genes Chromosomes Cancer. 2022 Jun;61(6):346-355
pubmed: 35388566