scholarly journals PROFIL EKSTRA PARU TUBERKULOSIS SECARA HISTOPATOLOGIK PADA FORMALIN FIXED PARAFFIN EMBEDDED (FFPE) DI PROVINSI JAMBI

2020 ◽  
Vol 8 (1) ◽  
pp. 60-66
Author(s):  
Fairuz Fairuz ◽  
Hasna Dewi ◽  
Humaryanto Humaryanto
Keyword(s):  
Extrapulmonary Tuberculosis ◽  
Granulomatous Inflammation ◽  
Public Health Problem ◽  
Global Public Health ◽  
Pathology Laboratory ◽  
Cross Sectional ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

ABSTRACT Background Extrapulmonary Tuberculosis (EPTB) is a condition in tissue outside the lung that is characterized pathologically with extensive involvement of lymphocyte inflammation cells, the presence of epitheloid granuloma cells in the langhans and the duration of the cancer. Tuberculosis (TB) remains a major global public health problem, with 1.5 million deaths every year worldwide.. Histopathologic variations in the appearance of the diagnosis of EPTB often overlap commonly with granulomatous inflammation. This study aims to describe the EPTB profile histopathologically on FFPE samples in Jambi province. Methods This research is a descriptive study with cross sectional technique, evaluating the histopathological picture of EPTB on formalin Fixed Paraffin Emdedded (FFPE) preparations. The study was conducted in February - August 2019 in the Anatomy Pathology Laboratory of the Faculty of Medicine and Health Sciences and FFPE samples originating from Hospitals in Jambi Province. Histopathological data are divided into 3 categories: non-specific chronic mastitis, granulomatous chronic mastitis and specific chronic mastitis. Histopathological variables were assessed by histopathological score. Result Obtained 72 FFPE EPTB tissues from hospitals in Jambi Province, mostly originating from lymph nodes as much as 58.3% followed by breasts as much as 16.5%. The most common histopathopathic picture is in accordance with tuberculosis (EPTB) as much as 54.2% and cases of granulomatous inflammation which is still high as much as 44.4%. Histopathological picture of EPTB fulfills all tuberulosis criteria (100%), in contrast to granulomatous inflammation only fulfills 2 criteria, namely lymphocytes and epithelioid. Conclusions Histopathological picture of extrapulmonary tuberculosis in histopathology for the most part still gives a classic picture. Key words : Histopathology, Extrapulmonal Tuberculosis, Formalin Fixed Paraffin Embedded (FFPE)     ABSTRAK Latar Belakang Ektrapulmonal Tuberkulosis (EPTB)  adalah suatu kondisi pada jaringan diluar paru  yang ditandai secara patologi dengan keterlibatan secara ekstensif  sebukan sel radang limfosit, adanya granuloma epitheloid  sel datia langhans dan masa perkijuan. Tuberkulosis (TB) tetap menjadi masalah kesehatan masyarakat global utama, dengan 1,5 juta kematian setiap tahun di seluruh dunia. Diagnosis untuk kasus EPTB  pada jaringan saat ini secara umum masih menggunakan pemriksaan patologi anatomi. Adanya berbagai variasi gambaran secara histopatologis mmebuat diagnosis EPTB seringkali tumpang tindih terumata dengan radang granulomatosa. Penelitian ini bertujuan untuk menggambarkan profil EPTB secara histopatologik pada sampel FFPE di provinsi Jambi. Metode Penelitian ini adalah penelitian deskriptif dengan teknik cross sectional, menilai gambaran histopatologis EPTB pada sediaan Formalin Fixed Paraffin Emdedded (FFPE).  Penelitian dilaksanakan pada Bulan Februari - Agustus 2019 di Laboratorium Patologi Anatomi Fakultas Kedokteran dan Ilmu Kesehatan dan sampel FFPE yang berasal dari Rumah Sakit di Provinsi Jambi..  Data histopatolgis dibagi menjadi 3 kategori yaitu : mastitis kronis non spesifik, mastitisn kronis granulomatosa dan mastitis kronis spesifik. Variabel histopatologi yang dinilai dengan skor histopatologis. Hasil Didapatkan 72 jaringan FFPE  EPTB dari Rumah Sakit di  Provinsi Jambi , paling banyak berasal dari  kelenjar getah bening sebanyak 58,3% diikuti dengan payudara sebanyak 16,5%. Gambaran histopatolgois paling banyak adalah sesuai dengan tuberculosis (EPTB) sebanyak 54,2% dan kasus radang granulomatosa  yang masih tinggi yaitu sebanyak 44,4%. Gambaran histopatologis EPTB memenuhi semua kriteria tuberulosis (100% ), berbeda dengan radang granulomatosa hanya memenuhi 2 kriteria yaitu sebukan limfiosit dan gambaran epitelioid. Kesimpulan gambaran histopatologis ekstra paru tuberkulosis secara histopatologis paling banyak ditemukan di kelenjar getah bening dan  sebagian besar masih memberikan gambaran yang klasik.   Kata kunci : Histopatologi,  Tuberkulosis Ekstra Paru , Formalin Fixed Parafin Embedded (FFPE)

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.

Comparison of Polymerase Chain Reaction With Histopathologic Features for Diagnosis of Tuberculosis in Formalin-Fixed, Paraffin-Embedded Histologic Specimens

2003 ◽  
Vol 127 (3) ◽  
pp. 326-330 ◽  
Author(s):  
Do Youn Park ◽  
Jee Yeon Kim ◽  
Kyung Un Choi ◽  
Jin Sook Lee ◽  
Chang Hun Lee ◽  
...  
Keyword(s):  
Chronic Inflammation ◽  
Granulomatous Inflammation ◽  
Giant Cells ◽  
Caseous Necrosis ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Type Giant ◽  
Tb Pcr ◽  
Formalin Fixed ◽  
Histopathologic Features

Abstract Objective.—To investigate the relationship between various histopathologic features and the results of the tuberculosis (TB)–polymerase chain reaction (PCR) method in routinely submitted histologic specimens for the histopathologic diagnosis of TB. Design.—We used 95 formalin-fixed, paraffin-embedded tissue blocks from 81 patients who were clinically suspected of having TB. We assessed the presence of histopathologic features including well-formed granuloma, poorly formed granuloma, caseous necrosis, and Langhans-type giant cells. We performed nested PCR for IS6110 and Ziehl-Neelsen staining for acid-fast bacilli (AFB). Results.—Of the 81 patients studied, 53 patients had chronic granulomatous inflammation, whereas 28 patients had only chronic inflammation without definite granulomatous inflammation. Of the 53 cases with chronic granulomatous inflammation, 17 (32%) were AFB positive and 36 (68%) were TB-PCR positive. Among cases with chronic granulomatous inflammation, the percentage that were positive and negative by TB-PCR differed significantly with the presence of various histopathologic features. All of the 13 cases with well-formed granuloma, caseous necrosis, and Langhans-type giant cells were TB-PCR positive; however, 10 (36%) of the 28 cases with chronic inflammation without granulomatous lesions were also TB-PCR positive. Conclusions.—TB-PCR is a rapid, sensitive method for the diagnosis of TB in routinely processed formalin-fixed, paraffin-embedded histologic specimens and is readily available in histopathology laboratories. We recommend use of TB-PCR when TB is suspected clinically, especially in cases of chronic inflammation without definite evidence of granulomatous inflammation.

Canine Hepatitis Associated with Intrahepatic Bacteria in Three Dogs

2018 ◽  
Vol 54 (1) ◽  
pp. 65-70 ◽  
Author(s):  
Joon Im ◽  
Derek P. Burney ◽  
Sean P. McDonough ◽  
Brigid Nicholson ◽  
Adam Eatroff ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Case Report ◽  
Fluorescence In Situ Hybridization ◽  
Antimicrobial Therapy ◽  
Granulomatous Inflammation ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Hematoxylin And Eosin ◽  
Formalin Fixed

ABSTRACT This case report describes the detection of intrahepatic bacteria in formalin-fixed paraffin-embedded histopathological sections from three dogs with neutrophilic, pyogranulomatous, or lymphoplasmacytic hepatitis and cholangiohepatitis. In each of these cases, eubacterial fluorescence in situ hybridization enabled colocalization of intrahepatic bacteria with neutrophilic and granulomatous inflammation in samples that were negative for bacteria when evaluated by routine hematoxylin and eosin histopathology augmented with histochemical stains. Positive responses to antimicrobial therapy were observed in of 2 out of 2 patients that were treated with antimicrobials. These findings suggest that eubacterial fluorescence in situ hybridization analysis of formalin-fixed paraffin-embedded histopathological sections is more sensitive than conventional histochemical stains for the diagnosis of bacteria-associated canine hepatitis.

scholarly journals Time and tumor type (primary or metastatic) do not influence the detection of BRAF/NRAS mutations in formalin fixed paraffin embedded samples from melanomas

2016 ◽  
Vol 54 (11) ◽  
Author(s):  
Miriam Potrony ◽  
Celia Badenas ◽  
Bénédicte Naerhuyzen ◽  
Paula Aguilera ◽  
Joan Anton Puig-Butille ◽  
...  
Keyword(s):  
Melanoma Patient ◽  
Primary Melanoma ◽  
Sentinel Lymph Nodes ◽  
Tumor Type ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Complete Sequencing ◽  
Formalin Fixed ◽  
Tumor Area

AbstractBackground:Methods:DNA was obtained from 144 FFPE samples (62 primary melanoma, 43 sentinel lymph nodes [SLN] and 39 metastasis).Results:Complete sequencing results were obtained from 75% (108/144) of the samples, and at least one gene was sequenced in 89% (128/144) of them.Conclusions:Preserving sufficient tumor area in FFPE blocks is important. It is necessary to keep the FFPE blocks, no matter their age, as they are necessary to decide the best treatment for the melanoma patient.

Results of first proficiency test for KRAS testing with formalin-fixed, paraffin-embedded cell lines in China

2014 ◽  
Vol 52 (12) ◽  
Author(s):  
Rui Zhang ◽  
Yanxi Han ◽  
Jie Huang ◽  
Liang Ma ◽  
Yulong Li ◽  
...  
Keyword(s):  
Cell Lines ◽  
Laboratory Testing ◽  
Proficiency Test ◽  
Cultured Cell ◽  
Proficiency Panel ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

AbstractLaboratory testing forArtificial FFPE samples were prepared from cultured cell lines to construct a proficiency panel of 10 samples covering eightThe percentages of mutant

scholarly journals Comparison of Whole Genome Amplification Methods for Analysis of DNA Extracted from Microdissected Early Breast Lesions in Formalin-Fixed Paraffin-Embedded Tissue

ISRN Oncology ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Nona Arneson ◽  
Juan Moreno ◽  
Vladimir Iakovlev ◽  
Arezou Ghazani ◽  
Keisha Warren ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Whole Genome Amplification ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Genomic Hybridization ◽  
Genome Amplification ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

To understand cancer progression, it is desirable to study the earliest stages of its development, which are often microscopic lesions. Array comparative genomic hybridization (aCGH) is a valuable high-throughput molecular approach for discovering DNA copy number changes; however, it requires a relatively large amount of DNA, which is difficult to obtain from microdissected lesions. Whole genome amplification (WGA) methods were developed to increase DNA quantity; however their reproducibility, fidelity, and suitability for formalin-fixed paraffin-embedded (FFPE) samples are questioned. Using aCGH analysis, we compared two widely used approaches for WGA: single cell comparative genomic hybridization protocol (SCOMP) and degenerate oligonucleotide primed PCR (DOP-PCR). Cancer cell line and microdissected FFPE breast cancer DNA samples were amplified by the two WGA methods and subjected to aCGH. The genomic profiles of amplified DNA were compared with those of non-amplified controls by four analytic methods and validated by quantitative PCR (Q-PCR). We found that SCOMP-amplified samples had close similarity to non-amplified controls with concordance rates close to those of reference tests, while DOP-amplified samples had a statistically significant amount of changes. SCOMP is able to amplify small amounts of DNA extracted from FFPE samples and provides quality of aCGH data similar to non-amplified samples.

scholarly journals A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Emily A Saunderson ◽  
Ann-Marie Baker ◽  
Marc Williams ◽  
Kit Curtius ◽  
J Louise Jones ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Preparation Method ◽  
Degraded Dna ◽  
Whole Genome ◽  
Library Preparation ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed ◽  
Library Preparation Method

Abstract The desire to analyse limited amounts of biological material, historic samples and rare cell populations has collectively driven the need for efficient methods for whole genome sequencing (WGS) of limited amounts of poor quality DNA. Most protocols are designed to recover double-stranded DNA (dsDNA) by ligating sequencing adaptors to dsDNA with or without subsequent polymerase chain reaction amplification of the library. While this is sufficient for many applications, limited DNA requires a method that can recover both single-stranded DNA (ssDNA) and dsDNA. Here, we present a WGS library preparation method, called ‘degraded DNA adaptor tagging’ (DDAT), adapted from a protocol designed for whole genome bisulfite sequencing. This method uses two rounds of random primer extension to recover both ssDNA and dsDNA. We show that by using DDAT we can generate WGS data from formalin-fixed paraffin-embedded (FFPE) samples using as little as 2 ng of highly degraded DNA input. Furthermore, DDAT WGS data quality was higher for all FFPE samples tested compared to data produced using a standard WGS library preparation method. Therefore, the DDAT method has potential to unlock WGS data from DNA previously considered impossible to sequence, broadening opportunities to understand the role of genetics in health and disease.

PDL-1 and immunohistochemistry markers in esophageal adenocarcinoma.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e15567-e15567
Author(s):  
Dawn E. Jaroszewski ◽  
Joanne Xiu ◽  
Zoran Gatalica ◽  
Staci Beamer ◽  
Melissa Stanton ◽  
...  
Keyword(s):  
Clinical Outcomes ◽  
Esophageal Adenocarcinoma ◽  
Neoadjuvant Treatment ◽  
Formalin Fixed Paraffin ◽  
Ffpe Tumor ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

e15567 Background: Esophageal adenocarcinoma (EAC) prognosis is poor and there is a need to identify patients that benefit most from neoadjuvant therapy. To examine the association of various biomarkers with clinical outcomes in neoadjuvant treatment of EAC, we retrospectively evaluated the biomarker expression (TS, ERCC1, TOPO1, PD-L1, PD-1) in patient matched formalin-fixed paraffin-embedded (FFPE) tumor samples. Methods: Immunohistochemistry of TS (TS106/4H4B1) , ERCC1 (Ab. 8F1), TOPO1 (1D6), PD-L1 (both 22c3 and SP142), PD-1 (NAT105), and chromogenic in-situ hybridization (CISH) of Her2 were performed on FFPE samples from 35 patients across 2 institutions at time of EAC diagnosis and after treatment when available. Retrospective clinical data and survival (5/2006-1/2016) was analyzed with a mean follow up of 110 months (range 22-306). Results: Overexpression (pre/post-treatment) of TS (60%/54%), ERCC1 (69%/16%), TOPO1 (74%/50%), PD-1 (54%/63%), PD-L1 (SP142) (2.9%/4%), PD-L1 (22c3) (0%/4%) and amplification of Her2 (18%/23%) were observed. Pretreatment observed PD-L1 levels were lower in our study (3%) when compared to other studies in EAC specimens (35%). Immunohistochemistry and changes observed after chemoradiation are reviewed in Table. No markers had significant correlation with prognosis however TS negative expression showed a non-significant (p=0.15) trend towards improved survival. Conclusions: Analyzing biomarkers in our neoadjuvant EAC cohort demonstrated a lower than expected PD-L1 positivity. In the largest cohort, to our knowledge, of patient matched FFPE tumor samples, we did not observe a statistically significant association between TS, ERCC1, TOPO1, PD-L1, or PD-1 with improved clinical outcomes. [Table: see text]

scholarly journals The Role of PCR in Diagnosis of a Rare Appendicular Tuberculosis and Mini Literature Review

2016 ◽  
Vol 2016 ◽  
pp. 1-3
Author(s):  
Asmerom Tesfamariam Sengal ◽  
Ahmed Abdalla Mohamedani ◽  
Hanan Hasaan Hussein ◽  
Alaa Kamal
Keyword(s):  
Public Health Problem ◽  
Abdominal Tuberculosis ◽  
Etiologic Agent ◽  
The Body ◽  
Formalin Fixed Paraffin ◽  
Granulomatous Lesions ◽  
Formalin Fixed Paraffin Embedded ◽  
Polymerase Chain ◽  
Formalin Fixed

Tuberculosis is a prevalent public health problem especially in the poor developing countries and results in significant mortality. Albeit tuberculosis almost always affects any organ or system of the body, abdominal tuberculosis is less frequent; moreover, tuberculous appendicitis is very rare with an incidence estimated at about 0.1–0.6% of all gastrointestinal tuberculosis. The purpose of this report was to present an unusual case of primary tuberculous appendicitis and the approach used for accurate diagnosis as well as a current update on the disease. We are reporting a 30-year-old male who presented with acute abdominal pain, fever, and vomiting and was admitted with the clinical diagnosis of acute appendicitis. Patient was investigated thoroughly and histopathologic examination was strongly suggestive of tuberculous appendicitis; however, Ziehl-Neelsen (ZN) was negative in tissue section. To confirm the diagnosis, molecular biology [polymerase chain reaction (PCR)] study was performed from the formalin fixed paraffin embedded (FFPE) appendicular tissue and revealed presence ofMycobacterium tuberculosis. As there are numerous differential diagnoses in granulomatous lesions of appendix and due to the fact that appendicular tuberculosis is a rare phenomenon; verification etiologic agent is crucial for appropriate management of the disease.

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