Novel hybridization- and tag-based error-corrected method for sensitive ctDNA mutation detection using ion semiconductor sequencing.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
06 04 2022
06 04 2022
Historique:
received:
22
11
2021
accepted:
24
03
2022
entrez:
7
4
2022
pubmed:
8
4
2022
medline:
9
4
2022
Statut:
epublish
Résumé
Circulating tumor DNA (ctDNA) analysis has emerged as a clinically useful tool for cancer diagnostics and treatment monitoring. However, ctDNA detection is complicated by low DNA concentrations and technical challenges. Here we describe our newly developed sensitive method for ctDNA detection on the Ion Torrent sequencing platform, which we call HYbridization- and Tag-based Error-Corrected sequencing (HYTEC-seq). This method combines hybridization-based capture with molecular tags, and the novel variant caller PlasmaMutationDetector2 to eliminate background errors. We describe the validation of HYTEC-seq using control samples with known mutations, demonstrating an analytical sensitivity down to 0.1% at > 99.99% specificity. Furthermore, to demonstrate the utility of this method in a clinical setting, we analyzed plasma samples from 44 patients with advanced pancreatic cancer, revealing mutations in 57% of the patients at allele frequencies as low as 0.23%.
Identifiants
pubmed: 35388068
doi: 10.1038/s41598-022-09698-5
pii: 10.1038/s41598-022-09698-5
pmc: PMC8986848
doi:
Substances chimiques
Biomarkers, Tumor
0
Circulating Tumor DNA
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
5816Informations de copyright
© 2022. The Author(s).
Références
J Clin Oncol. 2018 Oct 19;:JCO1800328
pubmed: 30339520
BMC Cancer. 2020 Oct 1;20(1):945
pubmed: 33004033
Sci Transl Med. 2015 Aug 26;7(302):302ra133
pubmed: 26311728
JCO Precis Oncol. 2019 Dec;3:1-9
pubmed: 35100678
J Clin Oncol. 2014 Feb 20;32(6):579-86
pubmed: 24449238
Nature. 2015 Feb 26;518(7540):495-501
pubmed: 25719666
Int J Cancer. 2010 Feb 1;126(3):589-98
pubmed: 19795462
Nat Med. 2014 May;20(5):548-54
pubmed: 24705333
Int J Cancer. 2020 Mar 1;146(5):1445-1456
pubmed: 31340061
Cancer Cell. 2017 Aug 14;32(2):169-184.e7
pubmed: 28810143
Genome Res. 2017 Mar;27(3):491-499
pubmed: 28100584
Nat Commun. 2018 Mar 1;9(1):896
pubmed: 29497091
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nat Biotechnol. 2016 May;34(5):547-555
pubmed: 27018799
Clin Cancer Res. 2017 Jan 1;23(1):116-123
pubmed: 27993964
Nat Med. 2019 Dec;25(12):1928-1937
pubmed: 31768066
Nat Med. 2019 May;25(5):738-743
pubmed: 31011204
Mol Oncol. 2016 Apr;10(4):635-43
pubmed: 26725968
N Engl J Med. 2013 Mar 28;368(13):1199-209
pubmed: 23484797
Bioinformatics. 2010 Mar 1;26(5):589-95
pubmed: 20080505
Clin Chem Lab Med. 2020 Jul 28;58(8):1341-1348
pubmed: 32623849
Bioinformatics. 2003 Feb 12;19(3):368-75
pubmed: 12584122
Nat Commun. 2015 Apr 09;6:6744
pubmed: 25855536
Nature. 2010 Apr 15;464(7291):993-8
pubmed: 20393554
Clin Chem. 2016 Nov;62(11):1492-1503
pubmed: 27624137
Sci Transl Med. 2014 Feb 19;6(224):224ra24
pubmed: 24553385
Sci Rep. 2020 Mar 5;10(1):4124
pubmed: 32139724
Sci Transl Med. 2017 Aug 16;9(403):
pubmed: 28814544
Clin Chem. 2015 Jan;61(1):79-88
pubmed: 25338683
Int J Cancer. 2017 May 15;140(10):2344-2350
pubmed: 28205231
Nat Protoc. 2014 Nov;9(11):2586-606
pubmed: 25299156