Development and analytical validation of a next-generation sequencing based microsatellite instability (MSI) assay.
MSI
NGS
microsatellite instability
next-generation sequencing
Journal
Oncotarget
ISSN: 1949-2553
Titre abrégé: Oncotarget
Pays: United States
ID NLM: 101532965
Informations de publication
Date de publication:
27 Aug 2019
27 Aug 2019
Historique:
received:
10
06
2019
accepted:
29
07
2019
entrez:
10
9
2019
pubmed:
10
9
2019
medline:
10
9
2019
Statut:
epublish
Résumé
We have developed and analytically validated a next-generation sequencing (NGS) assay to classify microsatellite instability (MSI) in formalin-fixed paraffin-embedded (FFPE) tumor specimens. The assay relies on DNA-seq evaluation of insertion/deletion (indel) variability at 29 highly informative genomic loci to estimate MSI status without the requirement for matched-normal tissue. The assay has a clinically relevant five-day turnaround time and can be conducted on as little as 20 ng genomic DNA with a batch size of up to forty samples in a single run. The MSI detection method was developed on a training set ( This assay provides clinicians with robust and reproducible NGS-based MSI testing without the need of matched normal tissue to inform clinical decision making for patients with solid tumors.
Sections du résumé
BACKGROUND
BACKGROUND
We have developed and analytically validated a next-generation sequencing (NGS) assay to classify microsatellite instability (MSI) in formalin-fixed paraffin-embedded (FFPE) tumor specimens.
METHODOLOGY
METHODS
The assay relies on DNA-seq evaluation of insertion/deletion (indel) variability at 29 highly informative genomic loci to estimate MSI status without the requirement for matched-normal tissue. The assay has a clinically relevant five-day turnaround time and can be conducted on as little as 20 ng genomic DNA with a batch size of up to forty samples in a single run.
RESULTS
RESULTS
The MSI detection method was developed on a training set (
SIGNIFICANCE
CONCLUSIONS
This assay provides clinicians with robust and reproducible NGS-based MSI testing without the need of matched normal tissue to inform clinical decision making for patients with solid tumors.
Identifiants
pubmed: 31497248
doi: 10.18632/oncotarget.27142
pii: 27142
pmc: PMC6718258
doi:
Types de publication
Journal Article
Langues
eng
Pagination
5181-5193Subventions
Organisme : NCI NIH HHS
ID : P30 CA016056
Pays : United States
Déclaration de conflit d'intérêts
CONFLICTS OF INTEREST SP, JA, FLL, BB, JH, VG, MKN, YW, MG, JMC, APS, CM, and STG are employees of OmniSeq, Inc. (Buffalo, NY, USA) and hold restricted stock in OmniSeq, Inc. JMC, CM, and STG are employees of Roswell Park Comprehensive Cancer Center (Buffalo, NY, USA), which is the majority shareholder of OmniSeq, Inc.
Références
N Engl J Med. 2003 Jul 17;349(3):247-57
pubmed: 12867608
J Natl Cancer Inst. 2004 Feb 18;96(4):261-8
pubmed: 14970275
Adv Anat Pathol. 2009 Nov;16(6):405-17
pubmed: 19851131
J Clin Oncol. 2010 Jul 10;28(20):3380-7
pubmed: 20516444
Eur J Hum Genet. 2014 Jul;22(7):875-80
pubmed: 24193342
Clin Chem. 2014 Sep;60(9):1192-9
pubmed: 24987110
N Engl J Med. 2015 Jun 25;372(26):2509-20
pubmed: 26028255
Curr Treat Options Oncol. 2015 Jul;16(7):30
pubmed: 26031544
PLoS One. 2015 Aug 07;10(8):e0132727
pubmed: 26252492
J Mol Diagn. 2015 Nov;17(6):705-14
pubmed: 26322950
N Engl J Med. 2015 Nov 12;373(20):1979
pubmed: 26559582
Nat Med. 2016 Nov;22(11):1342-1350
pubmed: 27694933
Nat Med. 2017 Jun;23(6):703-713
pubmed: 28481359
Nat Commun. 2017 Jun 06;8:15180
pubmed: 28585546
Science. 2017 Jul 28;357(6349):409-413
pubmed: 28596308
Lancet Oncol. 2017 Sep;18(9):1182-1191
pubmed: 28734759
Nat Biotechnol. 2017 Oct;35(10):951-959
pubmed: 28892075
Clin Chem. 2018 Jun;64(6):950-958
pubmed: 29632127
JCO Precis Oncol. 2017;2017:null
pubmed: 29850653
Annu Rev Genomics Hum Genet. 2019 Aug 31;20:293-307
pubmed: 30848956
Cancer Res. 1998 Nov 15;58(22):5248-57
pubmed: 9823339