scholarly journals Comparison of the miRNA expression profiles in fresh frozen and formalin-fixed paraffin-embedded tonsillar tumors

PLoS ONE ◽  
2017 ◽  
Vol 12 (6) ◽  
pp. e0179645 ◽  
Author(s):  
Zuzana Vojtechova ◽  
Jiri Zavadil ◽  
Jan Klozar ◽  
Marek Grega ◽  
Ruth Tachezy
Keyword(s):  
Mirna Expression ◽  
Expression Profiles ◽  
Formalin Fixed Paraffin ◽  
Mirna Expression Profiles ◽  
Formalin Fixed Paraffin Embedded ◽  
Fresh Frozen ◽  
Formalin Fixed

Application of micro-RNA (miRNA) expression profiles for prognostication in low-risk endometrial carcinoma (LEC).

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 5032-5032
Author(s):  
Johanne Ingrid Weberpals ◽  
Jaime Snowdon ◽  
Olga Bougie ◽  
Xiao Zhang ◽  
Victor Tron ◽  
...  
Keyword(s):  
Decision Tree ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Mirna Expression Profile ◽  
Micro Rna ◽  
Primary Surgery ◽  
Formalin Fixed Paraffin ◽  
Mirna Expression Profiles ◽  
Formalin Fixed Paraffin Embedded ◽  
Stage 1

5032 Background: Reliably predicting which LEC patients are most likely to recur is a challenge for the clinician with implications on adjuvant therapy. MiRNAs have been exploited for diagnosis and prognostication in a number of malignancies. We hypothesize that miRNA expression profiles differ in tumors from patients with recurrence compared to those without recurrence. Methods: The inclusion criteria for this study are informed consent, stage 1 disease, grade 1 or 2 tumors and endometrioid histology. RNA was extracted from formalin-fixed paraffin-embedded tissues and miRNA profiling was done using Agilent Human miRNA. Differentially expressed miRNAs were identified using GeneSpring GX software and the two groups were compared using the student t-test. Results: The expression levels of 866 miRNAs were determined from LEC patients with recurrence (n=15) and without recurrence (n=16). The mean follow-up interval was 61.5 months. The average age of cancer diagnosis for patients with and without recurrence was 60.2 (range 42-75) and 59.7 (range 44-86), respectively (p=0.91). Three of 15 patients with recurrence and 6 of 16 patients without recurrence received adjuvant brachytherapy following their primary surgery (p=0.43). 17 miRNAs were identified which can distinguish between the tumors with recurrence and those without recurrence (p<0.05). MiR-146a, miR-18a, miR-222, and miR-30a showed the highest fold change difference (>5 fold) in the tumors with recurrence compared to that did not recur. A decision tree prediction model for recurrent LEC was developed where a miRNA cutoff was used as a branch in the decision tree. This model identified those patients who were most likely to recur based on the expression of 4 dysregulated miRNAs (miR-222, miR-361-3p, miR-181c and miR-125b). Conclusions: These preliminary results show the miRNA expression profile differs among LEC and can be used to distinguish an aggressive sub-group. Should future validation studies confirm this result, this information would be valuable in the design of a biomarker study to help decide which patients would benefit most from extended adjuvant treatment.

scholarly journals Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Kyrillus S. Shohdy ◽  
Rohan Bareja ◽  
Michael Sigouros ◽  
David C. Wilkes ◽  
Princesca Dorsaint ◽  
...  
Keyword(s):  
Molecular Subtype ◽  
Expression Profiles ◽  
Exome Capture ◽  
Clinical Samples ◽  
Precision Oncology ◽  
Rna Seq ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Fresh Frozen ◽  
Formalin Fixed

AbstractThe availability of fresh frozen (FF) tissue is a barrier for implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. We performed transcriptomic analysis of 32 FFPE tumor samples from 11 patients using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to the TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. The Spearman’s correlation coefficients between the global expression profiles of the three capture-based methods from FFPE and matched FF-TruSeq were high (rho = 0.72–0.9, p < 0.05). A significant correlation between the expression of key immune genes between individual capture-based methods and FF-TruSeq (rho = 0.76-0.88, p < 0.05) was observed. All exome capture-based methods reliably detected outlier expression of actionable gene transcripts, including ERBB2, MET, NTRK1, and PPARG. In urothelial cancer samples, the Agilent assay was associated with the highest molecular subtype concordance with FF-TruSeq (Cohen’s k = 0.7, p < 0.01). The Agilent and IDT assays detected all the clinically relevant fusions that were initially identified in FF-TruSeq. All FFPE exome capture-based methods had comparable performance and concordance with FF-TruSeq. Our findings will enable the implementation of RNA-seq in the clinic to guide precision oncology approaches.

scholarly journals Monoclonal and Polyclonal Antibodies for Immunohistochemical Detection of Bovine Parainfluenza Type 3 Virus in Frozen and Formalin-Fixed Paraffin-Embedded Tissues

1992 ◽  
Vol 4 (4) ◽  
pp. 393-399 ◽  
Author(s):  
Deborah M. Haines ◽  
Jane C. Kendall ◽  
Brad W. Remenda ◽  
Michelle M. Breker-Klassen ◽  
Edward G. Clark
Keyword(s):  
Polyclonal Antibodies ◽  
Accurate Identification ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Fresh Frozen ◽  
Type 3 ◽  
Murine Monoclonal Antibodies ◽  
Formalin Fixed ◽  
Immunohistochemical Testing

Accurate identification of bovine Parainfluenza type 3 virus in bovine respiratory disease requires dependable, sensitive, and specific techniques for detection in affected animals. Immunohistochemical testing can be a rapid and reliable means of demonstration of virus in tissues from suspect cases; however, this procedure is dependent upon the quality of the antisera directed against the viral antigens. The production of rabbit polyclonal and murine monoclonal antibodies directed against bovine Parainfluenza type 3 virus and techniques for their use in fresh-frozen and formalin-fixed paraffin-embedded tissues in immunofluorescence and immunoperoxidase-based immunohistochemical tests are described.

scholarly journals miRNA expression profiling in formalin-fixed paraffin-embedded endometriosis and ovarian cancer samples

2017 ◽  
Vol Volume 10 ◽  
pp. 4225-4238 ◽  
Author(s):  
Ovidiu-Leonard Braicu ◽  
Liviuta Budisan ◽  
Rares Buiga ◽  
Ancuta Jurj ◽  
Patriciu Achimas-Cadariu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Mirna Expression Profiling ◽  
Formalin Fixed
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