Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens.
Todai OncoPanel
clinical sequencing
junction capture method
molecular profiling
personalized medicine
Journal
Cancer science
ISSN: 1349-7006
Titre abrégé: Cancer Sci
Pays: England
ID NLM: 101168776
Informations de publication
Date de publication:
Apr 2019
Apr 2019
Historique:
received:
13
11
2018
revised:
17
01
2019
accepted:
30
01
2019
pubmed:
10
2
2019
medline:
17
4
2019
entrez:
10
2
2019
Statut:
ppublish
Résumé
Tumor molecular profiling is becoming a standard of care for patients with cancer, but the optimal platform for cancer sequencing remains undetermined. We established a comprehensive assay, the Todai OncoPanel (TOP), which consists of DNA and RNA hybridization capture-based next-generation sequencing panels. A novel method for target enrichment, named the junction capture method, was developed for the RNA panel to accurately and cost-effectively detect 365 fusion genes as well as aberrantly spliced transcripts. The TOP RNA panel can also measure the expression profiles of an additional 109 genes. The TOP DNA panel was developed to detect single nucleotide variants and insertions/deletions for 464 genes, to calculate tumor mutation burden and microsatellite instability status, and to infer chromosomal copy number. Clinically relevant somatic mutations were identified in 32.2% (59/183) of patients by prospective TOP testing, signifying the clinical utility of TOP for providing personalized medicine to cancer patients.
Identifiants
pubmed: 30737998
doi: 10.1111/cas.13968
pmc: PMC6447855
doi:
Substances chimiques
Biomarkers, Tumor
0
Oncogene Proteins, Fusion
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1464-1479Subventions
Organisme : Japan Agency for Medical Research and Development
ID : 17kk0205003h0002
Organisme : Japan Agency for Medical Research and Development
ID : JP17am0001001
Organisme : Japan Agency for Medical Research and Development
ID : JP17ck0106252
Organisme : Japan Agency for Medical Research and Development
ID : JP17cm0106502
Organisme : Sysmex Corporation
Organisme : Eisai
Informations de copyright
© 2019 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.
Références
Cancer Discov. 2014 Apr;4(4):415-22
pubmed: 24469108
Science. 2013 Mar 29;339(6127):1546-58
pubmed: 23539594
PLoS One. 2014 May 30;9(5):e98187
pubmed: 24878701
Nat Genet. 2014 Jun;46(6):583-7
pubmed: 24816255
Br J Haematol. 1995 May;90(1):138-46
pubmed: 7786776
BMC Cancer. 2017 Apr 4;17(1):241
pubmed: 28376728
Bioinformatics. 2014 Apr 1;30(7):1015-6
pubmed: 24371154
Proc Natl Acad Sci U S A. 1986 Mar;83(6):1807-11
pubmed: 3513189
Nat Med. 2012 Feb 12;18(3):378-81
pubmed: 22327623
Nat Methods. 2007 Nov;4(11):931-6
pubmed: 17934468
Genes Chromosomes Cancer. 2012 May;51(5):510-20
pubmed: 22337624
Nat Genet. 2007 Dec;39(12):1522-7
pubmed: 17982454
Nat Med. 2013 Nov;19(11):1469-1472
pubmed: 24162815
Nat Methods. 2007 Nov;4(11):903-5
pubmed: 17934467
Toxicol Sci. 2016 Dec;154(2):202-213
pubmed: 27562560
Nat Methods. 2007 Nov;4(11):907-9
pubmed: 17934469
Cell. 2018 Apr 5;173(2):371-385.e18
pubmed: 29625053
Genome Biol. 2010;11(10):R99
pubmed: 20932289
Ultrastruct Pathol. 2003 Sep-Oct;27(5):363-8
pubmed: 14708728
Nat Genet. 2014 Dec;46(12):1267-73
pubmed: 25362482
Cell. 2018 Apr 5;173(2):305-320.e10
pubmed: 29625049
Nat Rev Cancer. 2011 Jul 14;11(8):541-57
pubmed: 21753790
Nat Med. 2017 Jun;23(6):703-713
pubmed: 28481359
JAMA Oncol. 2016 Jan;2(1):104-11
pubmed: 26556299
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Nat Med. 2012 Feb 12;18(3):382-4
pubmed: 22327622
Proc Natl Acad Sci U S A. 2007 May 29;104(22):9387-92
pubmed: 17517648
Nat Biotechnol. 2009 Feb;27(2):182-9
pubmed: 19182786
Genome Res. 2015 Sep;25(9):1372-81
pubmed: 26253700
Cell. 2018 Apr 5;173(2):355-370.e14
pubmed: 29625052
Leukemia. 2018 Feb;32(2):273-284
pubmed: 28701730
Clin Cancer Res. 2014 Aug 1;20(15):4107-14
pubmed: 24850843
Nat Methods. 2013 Jul;10(7):623-9
pubmed: 23685885
Nat Med. 2014 Dec;20(12):1479-84
pubmed: 25384085
Nature. 2007 Aug 2;448(7153):561-6
pubmed: 17625570
Genes (Basel). 2015 Feb 12;6(1):46-59
pubmed: 25685876
Cell. 2017 Nov 16;171(5):1042-1056.e10
pubmed: 29056344
Nature. 2013 Aug 22;500(7463):415-21
pubmed: 23945592
Cancer Discov. 2015 Aug;5(8):850-9
pubmed: 25971938
J Thorac Oncol. 2016 Jan;11(1):39-51
pubmed: 26762738
Cancer Sci. 2019 Apr;110(4):1464-1479
pubmed: 30737998
Cancer Discov. 2015 Aug;5(8):842-9
pubmed: 25971939
Nat Med. 2012 Feb 12;18(3):375-7
pubmed: 22327624
Genes Chromosomes Cancer. 1999 May;25(1):6-15
pubmed: 10221334
Clin Cancer Res. 2019 Jan 1;25(1):378-389
pubmed: 30279230