OBJECTIVES: The traditional processing method for paraffin-embedded tissues is time-consuming, while the ultrasonic rapid processing method has a short processing time. However, its effects on tissue proteins, DNA, and RNA remain unclear. This study aims to evaluate the effects of the ultrasonic rapid processing method on proteins, DNA, and RNA in paraffin-embedded tissues through hematoxylin and eosin (HE) staining, immunohistochemical staining, and molecular pathological detection. METHODS: Surgical specimens from patients with breast cancer, colorectal cancer, lung cancer, signet-ring cell gastric cancer, liver cancer, and other tumors were selected. Two tissue blocks (1 to 3 mm in diameter) were obtained from each specimen (previously processed and diagnosed by routine pathology). One block was assigned to the control group (traditional processing method), and the other was the experimental group (ultrasonic rapid processing method). Via HE staining, immunohistochemical staining, DNA quality fragment analysis, fluorescent in situ hybrid for HER2 gene expression test, second-generation sequencing for EGFR and ALK gene mutation test, real-time reverse transcription PCR (real-time RT-PCR) for prognosis detection of breast cancer etc, the difference between 2 groups was compared, and further impact of the ultrasonic rapid processing method was analyzed. RESULTS: Compared with the control group, the ultrasound-assisted rapid method efficiently completed fixation, dehydration, clearing, and paraffin embedding, significantly reducing sample preparation time before pathological diagnosis. Results of HE staining, immunohistochemistry, DNA fragment analysis, fluorescence in situ hybridization for HER2 gene, next-generation sequencing for EGFR and ALK gene, and real-time RT-PCR for breast cancer prognosis were entirely consistent with those of the control group. CONCLUSIONS The ultrasonic rapid processing method can quickly and effectively shorten the time for specimen processing before pathological diagnosis, and will not affect the DNA, RNA and proteins of the specimens. It can meet the subsequent HE staining, immunohistochemistry and molecular pathological detection.
Humans ; Paraffin Embedding/methods* ; Female ; RNA/analysis* ; DNA/analysis* ; Breast Neoplasms/pathology* ; Neoplasms/genetics* ; Ultrasonics/methods* ; Proteins/analysis*

OBJECTIVE: Assessing the accuracy of automated EasyNAT system for rapidly detecting paraffin-embedded tissue for the diagnosis of tuberculosis. METHODS: A retrospective analysis was conducted on 134 patients, comprising 101 with confirmed tuberculosis and 33 without tuberculosis, treated at Beijing Chest Hospital, Capital Medical University, between 2018 and 2022.The clinical diagnostic results served as the standard for assessing the diagnostic performance of the EasyNAT system in comparison to quantitative real-time polymerase chain reaction (qPCR) for tuberculosis detection in paraffin-embedded tissues.The evaluation criteria included sensitivity, specificity, positive predictive value, negative predictive value, and accuracy rate. RESULTS: Based on the clinical diagnostic results, the EasyNAT assay demonstrated a sensitivity of 87.1%(88/101, 95%CI: 79.2%-92.3%)and a specificity of 100.0%(33/33, 95%CI: 89.6%-100.0%).The positive predictive value, negative predictive value, and accuracy rate were 100% (88/88, 95%CI: 95.8%-100.0%), 71.7%(33/46, 95%CI: 57.5%-82.7%), and 90.3%(121/134, 95%CI: 84.1%-94.2%), respectively.In comparison, the qPCR assay exhibited a sensitivity of 96.0%(90.3%-98.5%)and a specificity of 100.0%(89.6%-100.0%).The positive predictive value, negative predictive value, and accuracy rate for qPCR were 100.0%(96.2%-100.0%), 89.2%(75.3%- 95.7%), and 97.0%(92.6%-98.8%).The Cohen's kappa value of 0.84 indicated substantial agreement between EasyNAT and qPCR.The detection rate of tuberculosis using this method was 86.4%(38/44, 95%CI: 73.3%-93.6%), while the detection rate for extrapulmonary tuberculosis was 87.7%(50/57, 95%CI: 76.8%-93.9%).In comparison, qPCR showed a detection rate of 97.7%(88.2%- 99.6%) for pulmonary tuberculosis and 94.7%(85.6%-98.6%)for extrapulmonary tuberculosis.There was no statistically significant difference in the detection results between the method and qPCR for both pulmonary and extrapulmonary tuberculosis(P>0.05).Importantly, the EasyNAT detection combined nucleic acid extraction, amplification, and analysis into one process.Compared with traditional qPCR methods, manual operation time was reduced by 2 hours, leading to an overall reduction in total testing time by 3 hours. CONCLUSION The EasyNAT nucleic acid rapid detection system can quickly, conveniently, and accurately detect Mycobacterium tuberculosis DNA in paraffin-embedded tissues, demonstrating significant clinical utility in the pathological diagnosis of tuberculosis.
Humans ; Retrospective Studies ; Paraffin Embedding ; Sensitivity and Specificity ; Tuberculosis/microbiology* ; Real-Time Polymerase Chain Reaction ; Mycobacterium tuberculosis/genetics* ; Predictive Value of Tests ; Nucleic Acid Amplification Techniques/methods* ; Female ; Male

No abstract available.
Adult ; Aged ; Base Sequence ; Bone Marrow/metabolism/pathology ; Female ; Formaldehyde/chemistry ; Gene Frequency ; Humans ; Male ; Middle Aged ; Multiple Myeloma/diagnosis/genetics ; Mutation ; Myeloid Differentiation Factor 88/chemistry/*genetics/metabolism ; Paraffin Embedding ; Sequence Analysis, DNA/*methods ; Waldenstrom Macroglobulinemia/diagnosis/genetics

OBJECTIVETo analyze the effect of special staining and immunohistochemical staining in distinguishing the types of renal amyloidosis to improve the diagnosis accuracy.

METHODSCongo red staining with different methods, and immunohistochemical staining of Kappa, Lambda and Amyloid A with different antigen retrieval methods were used for staining frozen and paraffin-embedded renal tissue sections.

RESULTSWright's Congo red staining produced a better contrast and a higher resolution and showed a greater stability than the other 2 methods after repeated use for staining the renal tissue sections (P<0.05). Immunofluorescent staining produced better results in frozen renal tissue sections than in paraffin-embedded tissues. Immunofluorescent staining produced had better performance than immunohistochemical staining in paraffin-embedded tissues. The retrieval effect with protein kinase K was the best among the antigen retrieval methods in paraffin-embedded tissues.

CONCLUSIONWright's Congo red staining is better than the other 2 methods in diagnosing renal amyloidosis. Immunohistochemical staining of Kappa, Lambda and Amyloid A in frozen renal tissue sections is necessary to discriminate the types of renal amyloidosis. For paraffin-embedded renal tissues, antigen retrieval using protein kinase K is better than the other 2 methods.

Amyloidosis ; classification ; diagnosis ; pathology ; Coloring Agents ; Congo Red ; Fluorescent Antibody Technique ; methods ; Frozen Sections ; Humans ; Immunohistochemistry ; Kidney ; pathology ; Kidney Diseases ; classification ; diagnosis ; pathology ; Paraffin Embedding ; Staining and Labeling ; methods

OBJECTIVETo use array-based comparative genomic hybridization (aCGH) technology to study the molecular cytogenetic abnormalities of anaplastic large cell lymphoma (ALCL) at genome level.

METHODSALK protein expression and molecular genetic abnormalities were detected by immunohistochemistry and fluorescence in situ hybridization, respectively, in 25 cases of ALCL. Any chromosomal gains/losses were detected by aCGH and correlated with ALK status.

RESULTSaCGH showed that chromosomal alterations in all 25 ALCL cases, and the frequency of chromosomal gains was higher than that of the losses. Chromosomal gains at 5p13.2, 3q21.1, 2q21.3, 3p25.1, 14q32.33, and 17q21.2 regions were detected in more than 50% of the ALCL cases; gains at 4q27, 6p22.1, 20p11.21, 2q22.3, 4q35.1, 1p36.22, 8p23.1, 8p12, 11q14.1, 12q13.13, and 19p13.3 regions were detected in 30%-50% of the ALCL cases; chromosomal losses at 3q26.1 and 3q26.31 regions were detected in 36.0% (9/25) and 24.0% (6/25) of the ALCL cases, respectively. Chromosomal gains at 2q21.3, 6p22.1 and 3p25.1 regions showed significant differences between ALK (+) and ALK (-) ALCL groups (P < 0.05).

CONCLUSIONSaCGH demonstrates complex molecular genetic variations in all ALCL cases. Gains at 2q21.3, 6p22.1 and 3p25.1 regions are significantly different between ALK (+) and ALK (-) ALCL groups, suggesting that the pathogenesis of ALK (+) and ALK (-) ALCL may involve different signaling pathway.

Adolescent ; Chromosome Aberrations ; Comparative Genomic Hybridization ; methods ; Female ; Gene Expression Profiling ; Humans ; In Situ Hybridization, Fluorescence ; Lymphoma, Large-Cell, Anaplastic ; enzymology ; genetics ; Male ; Paraffin Embedding ; Receptor Protein-Tyrosine Kinases ; genetics ; metabolism

OBJECTIVETo investigate the feasibility of real-time fluorescent quantitative (qPCR) assay in detecting mycobacterium tuberculosis complex (MTB) in paraffin embedded tissues for diagnostic purpose.

METHODSUsing qPCR assay, 1000 consecutive formalin-fixed and paraffin embedded (FFPE) tissues (from 2011 to 2012) suspected of MTB infection were tested by amplifying the MTB specific insertion sequence 6110 (IS6110). The specificity of the PCR product was confirmed by Sanger sequencing as compared with the MTB genomic DNA of the IS6110 sequence. Tissues with Ziehl-Neelsen acid-fast staining were used as control.

RESULTSIn the 1000 samples, 513 were positive for mycobacterium by Ziehl-Neelsen acid-fast staining (detection rate 51.3%); whereas 546 were MTB positive by qPCR assay (detection rate 54.6%). Concordance rate for both assays was 73.1%. The diagnosis rate increased by 14.4% by combinination of Ziehl-Neelsen acid-fast staining and qPCR results. More interestingly, by analyzing the Ziehl-Neelsen acid-fast staining and qPCR results three cases of M.leprae infection and four cases of non-tuberculous Mycobacterium (NTM) infection were identified.

CONCLUSIONSqPCR detection of MTB in FFPE tissue is more sensitive than Ziehl-Neelsen acid-fast staining assay. Combination of these two assays can increase the detection rate and also identify some rare cases of NTM infection.

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; DNA, Bacterial ; genetics ; Female ; Humans ; Male ; Middle Aged ; Mycobacterium tuberculosis ; genetics ; isolation & purification ; Paraffin Embedding ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Staining and Labeling ; methods ; Tuberculosis ; diagnosis ; microbiology ; Tuberculosis, Gastrointestinal ; diagnosis ; microbiology ; Tuberculosis, Lymph Node ; diagnosis ; microbiology ; Tuberculosis, Pulmonary ; diagnosis ; microbiology ; Young Adult

Ascitic Fluid ; cytology ; Cytological Techniques ; instrumentation ; methods ; Equipment Design ; Histocytological Preparation Techniques ; instrumentation ; methods ; Humans ; Paraffin Embedding ; Specimen Handling ; instrumentation ; methods

OBJECTIVETo map the frequency and types of EGFR gene mutations present in lung cancer tissues. To evaluate the clinical applicability of a novel real-time double-loop probe PCR of which the ADx-EGFR kit is based, and to compare its performance with traditional Sanger DNA sequencing in the detection of somatic mutations of tumor genes.

METHODSA total of 208 formalin-fixed paraffin-embedded (FFPE) tumor samples were tested. Genomic DNA of the tissue samples was extracted and purified, and subjected to both traditional PCR amplification, Sanger sequencing of EGFR gene in exon 18, 19, 20, 21, and ADx's EGFR mutation detection kit. The mutation rates for EGFR gene in exon 18, 19, 20, 21, as well as the frequency of each mutation detected by the two methods, were analyzed.

RESULTSThe traditional Sanger DNA sequencing technique was successfully performed in 196 out of 208 (94.2%) lung cancer samples, and 22 samples (11.2%) showed EGFR gene mutations. ADx-EGFR kit was successfully used in the lung cancers of all of the 208 cases (100.0%), and 40 samples (19.2%) showed mutations. In the lung cancer samples analyzed, mutations were mainly detected in the exon 19 and exon 21 L858R point mutation, i.e. 4.8% (10/208) and 11.6% (23/208) of total mutations, respectively, and the remaining mutations were rare.

CONCLUSIONSThe success rate of ADx-EGFR real-time PCR for formalin-fixed and paraffin-embedded tissues samples is significantly higher than that of Sanger sequencing (P < 0.01). There are significant differences between the two methods. ADx-EGFR real-time PCR shows a much higher successful detection rate and mutation rate of lung cancer tissues compared with that of Sanger sequencing. As a result, the real-time PCR with ADx-EGFR kit is proved to have a good clinical applicability and a strong advantage over the traditional Sanger DNA sequencing. It is an effective and reliable tool for clinical screening of somatic gene mutations in tumors.

DNA Mutational Analysis ; methods ; Exons ; Genes, erbB-1 ; Humans ; Lung Neoplasms ; genetics ; Paraffin Embedding ; Point Mutation ; Real-Time Polymerase Chain Reaction ; methods

Biopsy ; Histological Techniques ; instrumentation ; methods ; Humans ; Indicators and Reagents ; Paraffin Embedding ; Ultrasonics

Adult ; Aged ; Aged, 80 and over ; Carcinoma in Situ ; virology ; Carcinoma, Squamous Cell ; virology ; Female ; Human papillomavirus 16 ; isolation & purification ; Human papillomavirus 18 ; isolation & purification ; Humans ; Microarray Analysis ; methods ; Middle Aged ; Papillomaviridae ; isolation & purification ; Papillomavirus Infections ; diagnosis ; Paraffin Embedding ; Polymerase Chain Reaction ; methods ; Uterine Cervical Neoplasms ; virology