P1-07-21: Analysis of Molecular Markers by Immunohistochemistry (IHC) Method on Formalin Fixed Paraffin Embedded (FFPE) Tissues Could Predict Shorter Recurrence Free Survival (RFS) and Overall Survival (OS) among Patients Who Have Received Adjuvant Chemotherapy for Early Breast Cancer.

2011 ◽  
Author(s):  
M Moe ◽  
J Gee ◽  
P Finlay ◽  
R Mansel ◽  
R Adams
Keyword(s):  
Breast Cancer ◽  
Overall Survival ◽  
Molecular Markers ◽  
Adjuvant Chemotherapy ◽  
Recurrence Free Survival ◽  
Free Survival ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

scholarly journals Molecular Markers for Prostate Cancer in Formalin-Fixed Paraffin-Embedded Tissues

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Tamara Sequeiros ◽  
Marta García ◽  
Melania Montes ◽  
Mireia Oliván ◽  
Marina Rigau ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Markers ◽  
Tumor Grade ◽  
Developed Countries ◽  
Response To Therapy ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

Prostate cancer (PCa) is the most frequently diagnosed type of cancer in developed countries. The decisive method of diagnosis is based on the results of biopsies, morphologically evaluated to determine the presence or absence of cancer. Although this approach leads to a confident diagnosis in most cases, it can be improved by using the molecular markers present in the tissue. Both miRNAs and proteins are considered excellent candidates for biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues, due to their stability over long periods of time. In the last few years, a concerted effort has been made to develop the necessary tools for their reliable measurement in these types of samples. Furthermore, the use of these kinds of markers may also help in establishing tumor grade and aggressiveness, as well as predicting the possible outcomes in each particular case for the different treatments available. This would aid clinicians in the decision-making process. In this review, we attempt to summarize and discuss the potential use of microRNA and protein profiles in FFPE tissue samples as markers to better predict PCa diagnosis, progression, and response to therapy.

scholarly journals Agreement in Breast Cancer Classification between Microarray and Quantitative Reverse Transcription PCR from Fresh-Frozen and Formalin-Fixed, Paraffin-Embedded Tissues

2007 ◽  
Vol 53 (7) ◽  
pp. 1273-1279 ◽  
Author(s):  
Michael Mullins ◽  
Laurent Perreard ◽  
John F Quackenbush ◽  
Nicholas Gauthier ◽  
Steven Bayer ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Training Set ◽  
Pcr Assay ◽  
Gene Set ◽  
Qrt Pcr ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Fresh Frozen ◽  
Ffpe Tissues ◽  
Formalin Fixed

Abstract Background: Microarray studies have identified different molecular subtypes of breast cancer with prognostic significance. To transition these classifications into the clinical laboratory, we have developed a real-time quantitative reverse transcription (qRT)-PCR assay to diagnose the biological subtypes of breast cancer from fresh-frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) tissues. Methods: We used microarray data from 124 breast samples as a training set for classifying tumors into 4 previously defined molecular subtypes: Luminal, HER2+/ER−, basal-like, and normal-like. We used the training set data in 2 different centroid-based algorithms to predict sample class on 35 breast tumors (test set) procured as FF and FFPE tissues (70 samples). We classified samples on the basis of large and minimized gene sets. We used the minimized gene set in a real-time qRT-PCR assay to predict sample subtype from the FF and FFPE tissues. We evaluated primer set performance between procurement methods by use of several measures of agreement. Results: The centroid-based algorithms were in complete agreement in classification from FFPE tissues by use of qRT-PCR and the minimized “intrinsic” gene set (40 classifiers). There was 94% (33 of 35) concordance between the diagnostic algorithms when comparing subtype classification from FF tissue by use of microarray (large and minimized gene set) and qRT-PCR data. We found that the ratio of the diagonal SD to the dynamic range was the best method for assessing agreement on a gene-by-gene basis. Conclusions: Centroid-based algorithms are robust classifiers for breast cancer subtype assignment across platforms and procurement conditions.

scholarly journals Higher PD-L1 Immunohistochemical Detection Signal in Frozen Compared to Matched Paraffin-Embedded Formalin-Fixed Tissues

Antibodies ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 24
Author(s):  
Hazem Ghebeh ◽  
Fatmah A. Mansour ◽  
Dilek Colak ◽  
Akram A. Alfuraydi ◽  
Amal A. Al-Thubiti ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Immunohistochemical Detection ◽  
Breast Cancer Patients ◽  
Preservation Method ◽  
Detection Technology ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
The Impact ◽  
Formalin Fixed

Purpose: Response to anti-PD-L1/PD-1 immunotherapy correlates with PD-L1 expression in breast cancer. However, the prevalence of PD-L1 positive breast cancer is variable, which could be due to differences in the population/cohort of patients tested or the preservation/detection technology used. To investigate this variability, we examined the effect of two tissue preservation methods on PD-L1 immunohistochemical detection in breast cancer. Methods: We compared PD-L1 expression in patient-matched frozen (FR) and formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer patients. PD-L1 expression was assessed using tumor proportion score (TPS, simply PD-L1 score), and case positivity was determined with PD-L1 score ≥5. Results: In FFPE tissues, PD-L1 was positive in 7–10% of tested patients, depending on the antibody used. In patient-matched FR tissues, the same antibodies showed positive PD-L1 expression in 20–30% of cases. The impact of the antibody tested on the rate of PD-L1 positivity (% of PDL1 positive cases) was minor, as evident in the near perfect concordance between PD-L1 score obtained using the different antibodies whether tested in FR or FFPE tissues. However, there was a systematic drop by an average of 13–20% in the PD-L1 score obtained in FFPE tissues compared to their patient-matched FR tissues. Conclusions: In the tested patient-matched cohort, there was consistently a higher PD-L1 score in FR than FFPE tissues, regardless of the antibody used, demonstrating a significant effect on PD-L1 detection due to the preservation method. These findings should inspire further work to improve the sensitivity of PD-L1 detection and possibly search for more sensitive antibodies in FFPE tissues.

scholarly journals Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers

2017 ◽  
Author(s):  
Suet Feung Chin ◽  
Angela Santoja ◽  
Marta Grzelak ◽  
Soomin Ahn ◽  
Stephen-John Sammut ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Whole Genome ◽  
Breast Cancer Patients ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

ABSTRACTPathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.

Longer Time Intervals from Diagnosis to Surgical Treatment in Breast Cancer: Associated Factors and Survival Impact

2018 ◽  
Vol 84 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Margaret Mariella ◽  
Charles W. Kimbrough ◽  
Kelly M. Mcmasters ◽  
Nicolas Ajkay
Keyword(s):  
Breast Cancer ◽  
Overall Survival ◽  
Adjuvant Chemotherapy ◽  
Time Interval ◽  
Recurrence Free Survival ◽  
Disease Specific Survival ◽  
Free Survival ◽  
Factors Associated ◽  
The Impact ◽  
Disease Specific

Time interval (TI) from breast cancer diagnosis to definitive surgery is increasing, but the impact on outcomes is not well understood. TI longer than 30 days is associated with a greater chance of delay of chemotherapy, which may impact survival. We sought to identify factors associated with longer TI and the influence on outcome measures. Methods: We examined TI for stage 0-III breast cancer patients treated between 2006 and 2015 at a university-based cancer center. Univariate and multivariate analyses were used to study factors associated with TI <30, 30 to 60, and >60 days. Kaplan–Meier plots were used to examine the effect of different TI on overall survival, disease-specific survival, and recurrence-free survival. Results: 1589 patients were included with a median follow-up of 47 months. Median TI was 32 days. Median TI increased in patients from 2011 to 2015 compared with those from 2006 to 2010 (35 vs 30 days, P < 0.001). On multivariate analysis, mastectomy (with or without reconstruction), MRI use, and increasing age were independent predictors of TI >30 days. There were no significant differences in overall survival, disease-specific survival, or recurrence-free survival. There was no association between TI >30 days and a subsequent delay >60 days to adjuvant chemotherapy (OR 1.04, 95% CI 0.72–1.52). Conclusions: TI has increased in the last five years. Patient characteristics, tumor biology, and stage do not influence TI, whereas age, mastectomy, and MRI use were all associated with longer TI. Longer TI does not appear to significantly delay adjuvant chemotherapy or influence short-term outcomes.

scholarly journals Outcomes of Radiotherapy for Mesenchymal and Non-Mesenchymal Subtypes of Gastric Cancer

Cancers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 943 ◽  
Author(s):  
Jeong Il Yu ◽  
Hee Chul Park ◽  
Jeeyun Lee ◽  
Changhoon Choi ◽  
Won Ki Kang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Adjuvant Chemoradiotherapy ◽  
Recurrence Free Survival ◽  
Curative Surgery ◽  
Free Survival ◽  
Rna Analysis ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Independent Variable ◽  
Formalin Fixed

Background: The purpose of this study was to evaluate the clinical outcomes following postoperative chemotherapy (XP) versus chemoradiotherapy (XP-RT) according to mesenchymal subtype based on RNA sequencing in gastric cancer (GC) in a cohort of the Adjuvant chemoRadioTherapy In Stomach Tumor (ARTIST) trial. Methods: Of the 458 patients enrolled in the ARTIST trial, formalin-fixed, paraffin-embedded (FFPE) specimens were available from 106 (23.1%) patients for RNA analysis. The mesenchymal subtype was classified according to a previously reported 71-gene MSS/EMT signature using the NanoString assay. Results: Of the 106 patients analyzed (50 in XP arm, 56 in XP-RT arm), 36 (34.0%) patients were categorized as mesenchymal subtype by NanoString assay. Recurrence-free survival (RFS, p = 0.009, hazard ratio (HR) = 2.11, 95% confidence interval (CI): 1.21–3.70) and overall survival (OS, p = 0.003, HR = 2.28, 95% CI: 1.31–3.96) were significantly lower in the mesenchymal subtype than in the non-mesenchymal subtype. In terms of post-operative radiotherapy (RT), mesenchymal subtype was not an independent variable to predict RFS or OS regardless to the assigned arm (XP with or without RT) in this patient cohort. However, there was a trend in the adjuvant XP arm, which showed higher OS than the XP-RT arm for the mesenchymal subtype and lower OS than the XP-RT arm for the non-mesenchymal subtype. Conclusions: We could not determine any significant differences between the mesenchymal and non-mesenchymal subtypes with respect to the effects of adjuvant XP with or without RT in gastric cancer following curative surgery.

scholarly journals Characterization of epididymal and testicular histologic lesions and use of immunohistochemistry and PCR on formalin-fixed tissues to detect Brucella canis in male dogs

2021 ◽  
pp. 104063872098688
Author(s):  
Andrea M. Camargo-Castañeda ◽  
Lauren W. Stranahan ◽  
John F. Edwards ◽  
Daniel G. Garcia-Gonzalez ◽  
Leonardo Roa ◽  
...  
Keyword(s):  
Accurate Diagnosis ◽  
Testicular Atrophy ◽  
Detection Techniques ◽  
Formalin Fixed Paraffin ◽  
Brucella Canis ◽  
Formalin Fixed Paraffin Embedded ◽  
Variable Sensitivity ◽  
Ffpe Tissues ◽  
Formalin Fixed

In male dogs, Brucella canis frequently causes epididymitis, ultimately resulting in testicular atrophy and infertility. Although B. canis predominantly affects the epididymis, the misleading term “orchitis” is still commonly used by clinicians. Of additional concern, diagnosis in dogs remains challenging because of variable sensitivity and specificity of serologic assays and fluctuations in bacteremia levels in infected dogs, reducing the sensitivity of blood culture. We describe here the histologic lesions in the scrotal contents of 8 dogs suspected of being infected with B. canis and clinically diagnosed with orchitis. We explored the possibility of using immunohistochemistry (IHC) and real-time PCR (rtPCR) in formalin-fixed, paraffin-embedded (FFPE) tissues to detect the presence of B. canis. Epididymitis of variable chronicity was identified in all 8 dogs, with only 3 also exhibiting orchitis. Using rtPCR, the presence of B. canis was identified in 4 of 8 dogs, with 3 of these 4 dogs also positive by IHC. These results suggest that rtPCR and IHC are promising techniques that can be used in FFPE tissues to detect B. canis when other detection techniques are unavailable. Additionally, accurate recognition of epididymitis rather than orchitis in suspect cases could aid in accurate diagnosis.

scholarly journals Overexpression of circulating MiR-30b-5p identifies advanced breast cancer

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Helena Estevão-Pereira ◽  
João Lobo ◽  
Sofia Salta ◽  
Maria Amorim ◽  
Paula Lopes ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Validation Cohort ◽  
Advanced Disease ◽  
Clinical Tool ◽  
Liquid Biopsies ◽  
Primary Tumors ◽  
Bodily Fluids ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

Abstract Background Breast cancer (BrC) remains the leading cause of cancer-related death in women, mainly due to recurrent and/or metastatic events, entailing the need for biomarkers predictive of progression to advanced disease. MicroRNAs hold promise as noninvasive cancer biomarkers due to their inherent stability and resilience in tissues and bodily fluids. There is increasing evidence that specific microRNAs play a functional role at different steps of the metastatic cascade, behaving as signaling mediators to enable the colonization of a specific organ. Herein, we aimed to evaluate the biomarker performance of microRNAs previously reported as associated with prognosis for predicting BrC progression in liquid biopsies. Methods Selected microRNAs were assessed using a quantitative reverse transcription-polymerase chain reaction in a testing cohort of formalin-fixed paraffin-embedded primary (n = 16) and metastatic BrC tissues (n = 22). Then, miR-30b-5p and miR-200b-3p were assessed in a validation cohort #1 of formalin-fixed paraffin-embedded primary (n = 82) and metastatic BrC tissues (n = 93), whereas only miR-30b-5p was validated on a validation cohort #2 of liquid biopsies from BrC patients with localized (n = 20) and advanced (n = 25) disease. ROC curve was constructed to evaluate prognostic performance. Results MiR-30b-5p was differentially expressed in primary tumors and paired metastatic lesions, with bone metastases displaying significantly higher miR-30b-5p expression levels, paralleling the corresponding primary tumors. Interestingly, patients with advanced disease disclosed increased circulating miR-30b-5p expression compared to patients with localized BrC. Conclusions MiR-30b-5p might identify BrC patients at higher risk of disease progression, thus, providing a useful clinical tool for patients’ monitoring, entailing earlier and more effective treatment. Nonetheless, validation in larger multicentric cohorts is mandatory to confirm these findings.

scholarly journals The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Michal Marczyk ◽  
Chunxiao Fu ◽  
Rosanna Lau ◽  
Lili Du ◽  
Alexander J. Trevarton ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Rna Sequencing ◽  
Rna Extraction ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
The Impact ◽  
Formalin Fixed

Abstract Background Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA. Methods Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche). All RNA samples underwent whole transcriptome RNA sequencing (wtRNAseq) and targeted RNA sequencing for 31 transcripts included in a signature of sensitivity to endocrine therapy. We assessed the effect of RNA extraction kit on the reliability of gene expression levels using linear mixed-effects model analysis, concordance correlation coefficient (CCC) and differential analysis. All protein-coding genes in the wtRNAseq and three gene expression signatures for breast cancer were assessed for concordance. Results Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from wtRNAseq between matched FF and FFPE samples (median CCC 0.63–0.66) and between technical replicates (median expression difference 0.13–0.22). More than half of genes were differentially expressed between FF and FFPE, but with low fold change (median |LFC| 0.31–0.34). Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used. The targeted RNAseq assay was concordant between FFPE and FF samples using any of the kits (CCC 0.91–0.96). Conclusions The selection of kit to purify RNA from FFPE did not influence the overall quality of results from wtRNAseq, thus variable reproducibility of gene signatures probably relates to the reliability of individual gene selected and possibly to the algorithm. Targeted RNAseq showed promising performance for clinical deployment of quantitative assays in breast cancer from FFPE samples, although numerical scores were not identical to those from wtRNAseq and would require calibration.

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