scholarly journals Single-day HER2neu amplification assessment using chip-based digital PCR in formalin-fixed paraffin-embedded breast carcinoma tissue

2018 ◽  
Vol Volume 10 ◽  
pp. 121-129
Author(s):  
Parth Shah ◽  
Shiva Murarka ◽  
Anupam Joshi ◽  
Bhavana Mehta ◽  
Vipal Parmar ◽  
...  
Keyword(s):  
Breast Carcinoma ◽  
Digital Pcr ◽  
Carcinoma Tissue ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Droplet Digital PCR Measurement of HER2 Copy Number Alteration in Formalin-Fixed Paraffin-Embedded Breast Carcinoma Tissue

2013 ◽  
Vol 59 (6) ◽  
pp. 991-994 ◽  
Author(s):  
Phillip Belgrader ◽  
Stephanie C Tanner ◽  
John F Regan ◽  
Ryan Koehler ◽  
Benjamin J Hindson ◽  
...  
Keyword(s):  
Breast Carcinoma ◽  
Copy Number ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Invasive Breast Carcinoma ◽  
Chromosome 17 ◽  
Analysis Tool ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

BACKGROUND Human epidermal growth factor receptor 2 (HER2) testing is routinely performed by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) analyses for all new cases of invasive breast carcinoma. IHC is easier to perform, but analysis can be subjective and variable. FISH offers better diagnostic accuracy and added confidence, particularly when it is used to supplement weak IHC signals, but it is more labor intensive and costly than IHC. We examined the performance of droplet digital PCR (ddPCR) as a more precise and less subjective alternative for quantifying HER2 DNA amplification. METHODS Thirty-nine cases of invasive breast carcinoma containing ≥30% tumor were classified as positive or negative for HER2 by IHC, FISH, or both. DNA templates for these cases were prepared from formalin-fixed paraffin-embedded (FFPE) tissues to determine the HER2 copy number by ddPCR. ddPCR involved emulsifying hydrolysis probe–based PCR reaction mixtures containing the ERBB2 [v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian); also known as HER2] gene and chromosome 17 centromere assays into nanoliter-sized droplets for thermal cycling and analysis. RESULTS ddPCR distinguished, through differences in the level of HER2 amplification, the 10 HER2-positive samples from the 29 HER2-negative samples with 100% concordance to HER2 status obtained by FISH and IHC analysis. ddPCR results agreed with the FISH results for the 6 cases that were equivocal by IHC analyses, confirming 2 of these samples as positive for HER2 and the other 4 as negative. CONCLUSIONS ddPCR can be used as a molecular-analysis tool to precisely measure copy number alterations in FFPE samples of heterogeneous breast tumor tissue.

Expression of proliferation genes in formalin-fixed paraffin-embedded (FFPE) tissue from breast carcinomas. Feasibility and relevance for a routine histopathology laboratory

2016 ◽  
Vol 70 (1) ◽  
pp. 25-32 ◽  
Author(s):  
Carla Thomas ◽  
Cleo Robinson ◽  
Ben Dessauvagie ◽  
Benjamin Wood ◽  
Greg Sterrett ◽  
...  
Keyword(s):  
Gene Expression ◽  
Breast Carcinoma ◽  
Expression Profiling ◽  
Proliferative Activity ◽  
Breast Cancers ◽  
Breast Carcinomas ◽  
Ki 67 ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

AimBreast carcinoma proliferative activity, histological grade and commercial molecular tests are all important in prognostication and treatment. There is a particular need for improved, standardised techniques for subclassification of grade 2 breast cancers into low-risk and high-risk prognostic groups. In this study we investigated whether gene expression profiling of five proliferation genes was feasible using breast cancer tissue in a clinical setting and whether these profiles could enhance pathological assessment.MethodsExpression of five proliferation gene mRNAs; Ki-67, STK 15, CCNB1, CCND1 and MYBL2, was quantified in 27 breast carcinomas and compared with Ki-67 proliferation index (PI) and Nottingham mitotic score.ResultsExpression of Ki-67, STK15 and MYBL2 mRNA showed moderate Spearman's correlation with Ki-67 PI (p<0.01), but CCND1 and CCNB1 showed weak, non-significant correlation. Individual gene expression did not associate with mitotic score but combined mRNA expression correlated with both Ki-67 PI (p=0.018) and mitotic score (p=0.03; 0.007).ConclusionsThis study confirms mRNA analysis in breast carcinoma formalin-fixed, paraffin-embedded samples is feasible and suggests gene expression profiling, using a small set of five proliferation genes, has potential in aiding histological grading or assessment of proliferative activity of breast cancers. To fully evaluate the clinical applicability of this approach, a larger cohort study with long-term follow-up data is required.

scholarly journals Protocol for PTEN Expression by Immunohistochemistry in Formalin-fixed Paraffin-embedded Human Breast Carcinoma

2010 ◽  
Vol 18 (4) ◽  
pp. 371-374 ◽  
Author(s):  
Rita A. Sakr ◽  
Violetta Barbashina ◽  
Mary Morrogh ◽  
Sarat Chandarlapaty ◽  
Victor P. Andrade ◽  
...  
Keyword(s):  
Breast Carcinoma ◽  
Human Breast Carcinoma ◽  
Pten Expression ◽  
Human Breast ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Droplet Digital PCR for Mutation Detection in Formalin-Fixed, Paraffin-Embedded Melanoma Tissues

2018 ◽  
Vol 20 (2) ◽  
pp. 240-252 ◽  
Author(s):  
Ashleigh C. McEvoy ◽  
Benjamin A. Wood ◽  
Nima M. Ardakani ◽  
Michelle R. Pereira ◽  
Robert Pearce ◽  
...  
Keyword(s):  
Mutation Detection ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Frequency of Epstein–Barr Virus DNA in Formalin-fixed Paraffin-embedded Tissue of Patients with Ductal Breast Carcinoma

2019 ◽  
Vol 20 (3) ◽  
pp. 687-692 ◽  
Author(s):  
Chia Sharifpour ◽  
Manoochehr Makvandi ◽  
Alireza Samabafzadeh ◽  
Abdolhassan Talaei-Zadeh ◽  
Nastaran Ranjbari ◽  
...  
Keyword(s):  
Breast Carcinoma ◽  
Epstein Barr Virus ◽  
Barr Virus ◽  
Ductal Breast Carcinoma ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Epstein Barr ◽  
Formalin Fixed

scholarly journals Accuracy and Clinical Relevance of Intra-Tumoral Fusobacterium nucleatum Detection in Formalin-Fixed Paraffin-Embedded (FFPE) Tissue by Droplet Digital PCR (ddPCR) in Colorectal Cancer

Diagnostics ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 114
Author(s):  
José Guilherme Datorre ◽  
Ana Carolina de Carvalho ◽  
Mariana Bisarro dos Reis ◽  
Monise dos Reis ◽  
Marcus Matsushita ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Relevance ◽  
Fusobacterium Nucleatum ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Detection Accuracy ◽  
Assay Optimization ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

The use of droplet digital PCR (ddPCR) to identify and quantify low-abundance targets is a significant advantage for accurately detecting potentially oncogenic bacteria. Fusobacterium nucleatum (Fn) is implicated in colorectal cancer (CRC) tumorigenesis and is becoming an important prognostic biomarker. We evaluated the detection accuracy and clinical relevance of Fn DNA by ddPCR in a molecularly characterized, formalin-fixed, paraffin-embedded (FFPE) CRC cohort previously analyzed by qPCR for Fn levels. Following a ddPCR assay optimization and an analytical evaluation, Fn DNA were measured in 139 CRC FFPE cases. The measures of accuracy for Fn status compared to the prior results generated by qPCR and the association with clinicopathological and molecular patients’ features were also evaluated. The ddPCR-based Fn assay was sensitive and specific to positive controls. Fn DNA were detected in 20.1% of cases and further classified as Fn-high and Fn-low/negative, according to the median amount of Fn DNA that were detected in all cases and associated with the patient’s worst prognosis. There was a low agreement between the Fn status determined by ddPCR and qPCR (Cohen’s Kappa = 0.210). Our findings show that ddPCR can detect and quantify Fn in FFPE tumor tissues and highlights its clinical relevance in Fn detection in a routine CRC setting.

scholarly journals Automated PCR detection of BRAF mutations in colorectal adenocarcinoma: a diagnostic test accuracy study

2015 ◽  
Vol 69 (5) ◽  
pp. 398-402 ◽  
Author(s):  
Richard Colling ◽  
Lai Mun Wang ◽  
Elizabeth Soilleux
Keyword(s):  
Digital Pcr ◽  
Turnaround Time ◽  
Test Accuracy ◽  
Braf Mutations ◽  
System A ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Accuracy Study ◽  
Automated Platform ◽  
Formalin Fixed

BackgroundTesting for BRAF mutations in colorectal carcinoma (CRC) is important in the screening pathway for Lynch syndrome and is of prognostic value to guide management. This is a diagnostic accuracy study of the Idylla system, a novel and automated alternative PCR system.Methods100 consecutive formalin-fixed, paraffin-embedded CRC resection cases were tested for BRAF mutations using the Idylla automated platform and compared with standard (Cobas) PCR.ResultsThe sensitivity of the Idylla BRAF test was 100% and the specificity was 96%. Only one discordant Idylla positive/standard PCR negative result occurred and on Droplet Digital PCR demonstrated a mutation not identified by traditional PCR in this case.ConclusionThis study has validated the Idylla system for BRAF testing in CRC and demonstrated a possibly greater sensitivity, in addition to cost effectiveness and shorter turnaround time, when compared with standard PCR.

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