Performance of a 50-gene next generation sequencing panel with post-centrifuge supernatant cytology fluid in non-small-cell lung cancer.
DNA stability
cytology
liquid based cytology
lung carcinoma
next generation sequencing
Journal
Diagnostic cytopathology
ISSN: 1097-0339
Titre abrégé: Diagn Cytopathol
Pays: United States
ID NLM: 8506895
Informations de publication
Date de publication:
Nov 2021
Nov 2021
Historique:
revised:
19
07
2021
received:
23
05
2021
accepted:
22
07
2021
pubmed:
3
8
2021
medline:
8
2
2022
entrez:
2
8
2021
Statut:
ppublish
Résumé
Liquid based cytology (LBC) specimens are increasingly utilized for molecular analysis, as results are comparable to molecular analysis performed on traditional specimens (biopsy or cell block). However, there are few studies demonstrating the long-term viability of DNA in LBC samples. In this study, a 50-gene next generation sequencing (NGS) panel was performed on DNA isolated from post-centrifuged supernatant LBC samples of cases of non-small-cell lung carcinoma. Comparison was made to results of an identical NGS panel performed on a concurrent clinical sample (biopsy or cell block). Quality parameters including DNA concentration, total reads, amplicons with reads under 450 and 350, and variant allele fraction were also compared. For a subset of LBC samples, DNA was isolated after being held for varying extended lengths of time after collection (up to 41 days) at 5°C and results compared. Results of NGS mutation analysis were concordant between LBC samples and clinical samples. DNA concentration was on average higher in the LBC samples compared to the clinical samples. The remaining metrics were more variable, but illustrated the adequacy of LBC samples for NGS testing. DNA isolated from LBC samples held for longer periods of time was of good concentration. NGS analysis was successfully performed on all samples, with concordance with results of clinical samples. DNA isolated directly from LBC fluid is suitable for NGS analysis. DNA is also stable in LBC preservative for extended periods of time before isolation and NGS analysis can subsequently be successfully performed.
Sections du résumé
BACKGROUND
BACKGROUND
Liquid based cytology (LBC) specimens are increasingly utilized for molecular analysis, as results are comparable to molecular analysis performed on traditional specimens (biopsy or cell block). However, there are few studies demonstrating the long-term viability of DNA in LBC samples.
METHODS
METHODS
In this study, a 50-gene next generation sequencing (NGS) panel was performed on DNA isolated from post-centrifuged supernatant LBC samples of cases of non-small-cell lung carcinoma. Comparison was made to results of an identical NGS panel performed on a concurrent clinical sample (biopsy or cell block). Quality parameters including DNA concentration, total reads, amplicons with reads under 450 and 350, and variant allele fraction were also compared. For a subset of LBC samples, DNA was isolated after being held for varying extended lengths of time after collection (up to 41 days) at 5°C and results compared.
RESULTS
RESULTS
Results of NGS mutation analysis were concordant between LBC samples and clinical samples. DNA concentration was on average higher in the LBC samples compared to the clinical samples. The remaining metrics were more variable, but illustrated the adequacy of LBC samples for NGS testing. DNA isolated from LBC samples held for longer periods of time was of good concentration. NGS analysis was successfully performed on all samples, with concordance with results of clinical samples.
CONCLUSION
CONCLUSIONS
DNA isolated directly from LBC fluid is suitable for NGS analysis. DNA is also stable in LBC preservative for extended periods of time before isolation and NGS analysis can subsequently be successfully performed.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1173-1178Informations de copyright
© 2021 Wiley Periodicals LLC.
Références
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