Consistency of the S5 DNA methylation classifier in formalin-fixed biopsies versus corresponding exfoliated cells for the detection of pre-cancerous cervical lesions.
Adolescent
Adult
Aged
Alphapapillomavirus
/ genetics
Area Under Curve
Biopsy
/ methods
Colposcopy
DNA Methylation
Female
Formaldehyde
Humans
Microfilament Proteins
/ genetics
Middle Aged
Precancerous Conditions
/ genetics
Sensitivity and Specificity
Sulfites
Tissue Fixation
Uterine Cervical Neoplasms
/ genetics
Young Adult
Uterine Cervical Dysplasia
/ genetics
DNA methylation
S5 classifier
biomarker
cervical cancer
formalin-fixed paraffin-embedded samples (FFPE)
Journal
Cancer medicine
ISSN: 2045-7634
Titre abrégé: Cancer Med
Pays: United States
ID NLM: 101595310
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
revised:
10
02
2021
received:
05
10
2020
accepted:
23
02
2021
pubmed:
13
3
2021
medline:
31
7
2021
entrez:
12
3
2021
Statut:
ppublish
Résumé
Methylation biomarkers are promising tools for diagnosis and disease prevention. The S5 classifier is aimed at the prevention of cervical cancer by the early detection of cervical intraepithelial neoplasia (CIN). S5 is based on pyrosequencing a promoter region of EPB41L3 and five late regions of HPV types 16, 18, 31, and 33 following bisulfite conversion of DNA. Good biomarkers should perform well in a variety of sample types such as exfoliated cells, fresh frozen or formalin-fixed paraffin-embedded (FFPE) materials. Here, we tested the performance of S5 on 315 FFPE biopsies with paired exfoliated cervical samples using four different conversion kits (Epitect Bisulfite, Epitect Fast Bisulfite, EZ DNA Methylation, and EZ DNA Methylation-Lightning). The S5 values from FFPE biopsies for all kits were significantly correlated with those obtained from their paired exfoliated cells. For the EZ DNA Methylation kit, we observed an average increased methylation of 4.4% in FFPE. This was due to incomplete conversion of DNA (73% for FFPE vs. 95% for cells). The other kits had a DNA conversion rate in FFPE similar to the cells (95%-97%). S5 performed well at discriminating <CIN2 lesions from CIN2+ lesions on the FFPE with all kits given optimized adjustments to the cut-off. The area under the curve (AUC) for S5 on FFPE was not significantly different from the paired cells (0.74-0.79 vs. 0.81). The best sensitivity and specificity were obtained for EZ DNA Methylation after the adjustment of the cut-off to reflect its lower conversion rate. Consistent methylation results can be obtained from FFPE material regardless of the conversion kit used. The S5 classifier performed as well on FFPE material as on exfoliated cells with adjusted cut-off allowing easier clinical implementation.
Identifiants
pubmed: 33710792
doi: 10.1002/cam4.3849
pmc: PMC8026949
doi:
Substances chimiques
EPB41L3 protein, human
0
Microfilament Proteins
0
Sulfites
0
Formaldehyde
1HG84L3525
hydrogen sulfite
OJ9787WBLU
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2668-2679Subventions
Organisme : Cancer Research UK
ID : C569/A16891
Pays : United Kingdom
Informations de copyright
© 2021 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.
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