scholarly journals Consistency of the S5 DNA methylation classifier in formalin‐fixed biopsies versus corresponding exfoliated cells for the detection of pre‐cancerous cervical lesions

2021 ◽  
Author(s):  
Caroline Reuter ◽  
Matthew Preece ◽  
Rawinder Banwait ◽  
Sabrina Boer ◽  
Jack Cuzick ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cervical Lesions ◽  
Exfoliated Cells ◽  
Formalin Fixed

scholarly journals DNA methylation of imprinted gene control regions in the regression of low-grade cervical lesions

2018 ◽  
Vol 143 (3) ◽  
pp. 552-560 ◽  
Author(s):  
Ayodele Gomih ◽  
Jennifer S. Smith ◽  
Kari E. North ◽  
Michael G. Hudgens ◽  
Wendy R. Brewster ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Low Grade ◽  
Gene Control ◽  
Cervical Lesions ◽  
Imprinted Gene ◽  
Control Regions

scholarly journals Triage of hrHPV-positive women: comparison of two commercial methylation-specific PCR assays

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Carolin Dippmann ◽  
Martina Schmitz ◽  
Kristina Wunsch ◽  
Stefanie Schütze ◽  
Katrin Beer ◽  
...  
Keyword(s):  
Dna Methylation ◽  
False Positive ◽  
Pap Smear ◽  
Intraepithelial Neoplasia ◽  
Molecular Diagnostic ◽  
Cervical Lesions ◽  
Detection Rates ◽  
Diagnostic Assays ◽  
Specific Pcr

Abstract Aim High-risk human papillomavirus (hrHPV)-based screening is becoming increasingly important, either by supplementing or replacing the traditional cytology-based cervical Pap smear. However, hrHPV screening lacks specificity, because it cannot differentiate between transient virus infection and clinically relevant hrHPV-induced disease. Therefore, reliable triage methods are needed for the identification of HPV-positive women with cervical intraepithelial neoplasia (CIN) in need of treatment. Promising tools discussed for the triage of these patients are molecular diagnostic tests based on epigenetic markers. Here, we compare the performance of two commercially available DNA methylation-based diagnostic assays—GynTect® and the QIAsure Methylation Test—in physician-taken cervical scrapes from 195 subjects. Findings Both GynTect® and the QIAsure Methylation Test detected all cervical carcinoma and carcinoma in situ (CIS). The differences observed in the detection rates between both assays for the different grades of cervical lesions (QIAsure Methylation Test: CIN1 26.7%, CIN2 27.8% and CIN3 74.3%; GynTect®: CIN1 13.3%, CIN2 33.3% and CIN3 60%) were not significant. Concerning the false-positive rates, significant differences were evident. For the healthy (NILM) hrHPV-positive group, the false-positive rates were 5.7% for GynTect® and 26.4% for QIAsure Methylation Test (p = 0.003) and for the NILM hrHPV-negative group 2.2% vs. 23.9% (p = 0.006), respectively. When considering hrHPV-positive samples only for comparison (n = 149), GynTect® delivered significantly higher specificity compared to the QIAsure Methylation Test for CIN2 + (87.6% vs. 67.4% (p < 0.001)) and CIN3 + (84.1% vs. 68.2% (p = 0.002)). Overall our findings suggest that DNA methylation-based tests are suitable for the triage of hrHPV-positive women. With the goal to provide a triage test that complements the limited specificity of HPV testing in HPV-based screening, GynTect® may be preferable, due to its higher specificity for CIN2+ or CIN3+ .

scholarly journals Analysis of DNA Methylation of Multiple Genes in Microdissected Cells From Formalin-fixed and Paraffin-embedded Tissues

2009 ◽  
Vol 57 (5) ◽  
pp. 477-489 ◽  
Author(s):  
Dimo Dietrich ◽  
Ralf Lesche ◽  
Reimo Tetzner ◽  
Manuel Krispin ◽  
Jörn Dietrich ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Ductal Carcinoma ◽  
Treatment Protocol ◽  
Tumor Infiltrating Lymphocytes ◽  
Tissue Samples ◽  
Bisulfite Treatment ◽  
Pcr Product ◽  
Reliable Quantification ◽  
Infiltrating Lymphocytes ◽  
Formalin Fixed

A procedure for simultaneous quantification of DNA methylation of several genes in minute amounts of sample material was developed and applied to microdissected formalin-fixed and paraffin-embedded breast tissues. The procedure is comprised of an optimized bisulfite treatment protocol suitable for samples containing only few cells, a multiplex preamplification and subsequent locus specific reamplification, and a novel quantitative bisulfite sequencing method based on the incorporation of a normalization domain into the PCR product. A real-time PCR assay amplifying repetitive elements was established to quantify low amounts of bisulfite-treated DNA. Ten prognostic and diagnostic epigenetic breast cancer bio-markers ( PITX2, RASSF1A, PLAU, LHX3, PITX3, LIMK1, SLITRK1, SLIT2, HS3ST2, and TFF1) were analyzed in tissue samples obtained from two patients with invasive ductal carcinoma of the breast. The microdissected samples were obtained from several areas within the tumor tissue, including intraductal and invasive carcinoma, adenosis, and normal ductal epithelia of adjacent normal tissue, as well as stroma, tumor infiltrating lymphocytes, and adipose tissue. Overall, reliable quantification was possible for all genes. For most genes, increased DNA methylation in invasive and intraductal carcinoma cells compared with other tissue components was observed. For TFF1, decreased methylation levels were observed in tumor cells. (J Histochem Cytochem 57:477–489, 2009)

Quantitative DNA methylation analysis of laser capture microdissected formalin-fixed and paraffin-embedded tissues

2010 ◽  
Vol 88 (1) ◽  
pp. 184-189 ◽  
Author(s):  
Jean-François Gagnon ◽  
François Sanschagrin ◽  
Simon Jacob ◽  
Andrée-Anne Tremblay ◽  
Louise Provencher ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Analysis ◽  
Laser Capture ◽  
Dna Methylation Analysis ◽  
Laser Capture Microdissected ◽  
Formalin Fixed

Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples

2016 ◽  
Vol 55 (1) ◽  
pp. 668-681 ◽  
Author(s):  
Stine T. Bak ◽  
Nicklas H. Staunstrup ◽  
Anna Starnawska ◽  
Tina F. Daugaard ◽  
Jens R. Nyengaard ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Chenglong Yu ◽  
Pierre-Antoine Dugué ◽  
James G. Dowty ◽  
Fleur Hammet ◽  
JiHoon E. Joo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Intraclass Correlation ◽  
Appropriate Technology ◽  
High Molecular Weight Dna ◽  
Illumina Humanmethylation450 ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
The Mean ◽  
Genomic Regions ◽  
Formalin Fixed

Abstract Objective In previous studies using Illumina Infinium methylation arrays, we have identified DNA methylation marks associated with cancer predisposition and progression. In the present study, we have sought to find appropriate technology to both technically validate our data and expand our understanding of DNA methylation in these genomic regions. Here, we aimed to assess the repeatability of methylation measures made using QIAseq targeted methyl panel and to compare them with those obtained from the Illumina HumanMethylation450 (HM450K) assay. We included in the analysis high molecular weight DNA extracted from whole blood (WB) and DNA extracted from formalin-fixed paraffin-embedded tissues (FFPE). Results The repeatability of QIAseq-methylation measures was assessed at 40 CpGs, using the Intraclass Correlation Coefficient (ICC). The mean ICCs and 95% confidence intervals (CI) were 0.72 (0.62–0.81), 0.59 (0.47–0.71) and 0.80 (0.73–0.88) for WB, FFPE and both sample types combined, respectively. For technical replicates measured using QIAseq and HM450K, the mean ICCs (95% CI) were 0.53 (0.39–0.68), 0.43 (0.31–0.56) and 0.70 (0.59–0.80), respectively. Bland–Altman plots indicated good agreement between QIAseq and HM450K measurements. These results demonstrate that the QIAseq targeted methyl panel produces reliable and reproducible methylation measurements across the 40 CpGs that were examined.

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