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Background: Recently, genetic mutations in surfactant protein C (SFTPC) have been linked to diffuse parenchymal lung diseases (DPLD). The present study investigated SFTPC mutations among Iranian patients with DPLD for the first time. Materials and Methods: In this study, we examined 28 patients diagnosed with DPLD. Patients were divided into two groups: 23 cases (82.1%) had interstitial lung disease (ILD), 7 (30.4%) of which were categorized as familial ILD, and 5 cases (17.9%) had pulmonary alveolar proteinosis (PAP). Genetic variations in the SFTPC gene were detected by direct DNA sequencing. Results: The mean (±SD) age of patients was 21.8 (± 17.1) years and 60.7% of the patients were male. Overall, 11 different mutations were detected in the SFTPC gene. Two novel mutations, c.202-43 G>A and c.416 G>C, were detected among patients. The c.201+49 C>T mutation showed a significant difference with the minor allele frequency (MAF) data. There was no significant difference between the most frequent mutations in Iranian patients and those of the general population in the world. The proximity analysis showed similarity between Iranian patients and patients of the African race. We did not find any correlation between SFTPC mutations and DPLD in the patients. Conclusion: It seems that the rs2070684 (c.201+49 C>T) mutation could be used as a specific genetic marker for distinguishing the Iranian population from other human races in the world. There was a correlation between some intronic variations and the development of disease. A new missense mutation, c.416 G>C that encodes Arg139Thr, could probably damage the protein structure and/or function and cause the signs and symptoms of DPLD. [ABSTRACT FROM AUTHOR]

Background & Objective: Various studies showed the use of epidermal growth factor receptors (EGFRs) gene mutations in the therapeutic plan of patients with advanced lung cancer. This study aimed to investigate the frequency and types of EGFR gene mutations among Iranian patients with lung adenocarcinoma referred to a specialized lung diseases hospital from 2014 to 2019. Methods: The data of all patients with lung adenocarcinoma referred to the Molecular Department of Masih Daneshvari Hospital Laboratory (National Research Institute of Tuberculosis and Lung Diseases) from 2014 to 2019 for EGFR mutation tests were collected. Patients' characteristics data and information on the frequency and types of EGFR gene mutations were obtained from the hospital information system (HIS). The collected data were analyzed using SPSS 25. Results: A total of 570 individuals (Mean age of 58.74, 51.6% Male) were included in the study; 113 out of 570 patients (19.8%) were diagnosed with gene mutation. In terms of the type of mutation, 65 participants (57%) showed deletion, 48 patients (42.1%) were diagnosed with replacement, and one (0.9%) case demonstrated both. Notably, the mutation rate detected among the female patients was significantly higher than the male ones (P=0.001); in particular, deletion type of mutation was found more among women, although both genders were the same in terms of the replacement frequency. However, the age had no effect on the mutation in this study (P=0.05). Conclusion: Among Iranian patients with lung adenocarcinoma, 19.8% harbored EGFR gene mutation. This mutation was found in association with lung cancer and could affect the patient's therapeutic plan. [ABSTRACT FROM AUTHOR]

Introduction: The purity of genomic DNA (gDNA) extracted from different clinical specimens optimizes sensitivity of polymerase chain reaction (PCR) assays. This study attempted to compare two different DNA extraction techniques namely salting-out and classic phenol-chloroform. Materials and Methods: Qualification of two different DNA extraction techniques for 634 clinical specimens highly suspected of having mycobacterial infection was performed. Genomic DNA was extracted from 330 clinical samples using phenol-chloroform and 304 by non-toxic salting-out. Qualification of obtained gDNA was done through amplification of internal controls, β-actin and β-globin. Results: β-actin-positive was detected in 279/330 (84%) and 272/304 (89%) samples by phenol-chloroform technique and salting-out, respectively. PCR inhibitor was found for the gDNA of 13/304 (4%) patient samples were negative by β-actin and β-globin tests via salting-out technique in comparison with gDNAs from 27/330 (8.5%) samples extracted by phenol-chloroform procedure. No statistically significant difference was found between phenolchloroform technique and salting-out for 385 sputum, 29 bronchoalveolar lavage (BAL), 105 gastric washing, and 38 body fluid (P=0.04) samples. This illustrates that both techniques have the same quality for extracting gDNA. Conclusion: This study discloses salting-out as a non-toxic DNA extraction procedure with a superior time-efficiency and cost-effectiveness in comparison with phenol-chloroform and it can be routinely used in resource-limited laboratory settings. [ABSTRACT FROM AUTHOR]

Background: Polymerase chain reaction (PCR) assay has widely used for the detection of tuberculosis (TB). This study tried to compare in-house PCR with some well-known commercial PCR kits for detection of TB agent. Methods: Clinical samples obtained from 620 TB suspected patients were analyzed for the diagnosis of Mycobacterium tuberculosis complex (MTC) by in-house PCR. All samples were obtained through pulmonary specimens consisted of 384 sputum, 148 bronchial aspirates and 88 pleural effusions. Results: Considering culture as a golden criterion, in which its diagnostic sensitivity and specificity of PCR assay were 87.7% and 85.6%, respectively. The findings of this study also indicate 22.1% (137/620) of the specimens were detected as MTC by PCR. Both PCR and culture confirmed presence of MTC in 57 of the samples. In comparison to culture, the diagnostic sensitivity of PCR for sputum was 87.5% (42/48), bronchial aspirates 100% (12/12), and 60% (3/5) for pleural effusions. The sensitivity of in-house PCR method is comparable with the sensitivity of Amplicor and Cobas TaqMan for MTC. Conclusion: The study illustrates the in-house PCR assay for detection of MTC has high sensitivity and specificity versus approved commercial kits. This could be reliable test in the diagnosis of MTC in resource-limited countries. [ABSTRACT FROM AUTHOR]

Background: Identification of gene rearrangements and clonality analysis are important techniques for the diagnosis of malignant lymphoproliferative diseases. These methods have various sensitivities based on the type of primer used and method of determination of polymerase chain reaction (PCR) products. This study aimed at determining the clonality of B cell non-Hodgkin lymphoma in Iranian patients using PCR method and 2 primers of FR2 and FR3., Materials and Methods: Paraffin embedded blocks of 67 patients with B cell lymphoma and 19 cases with lymphoid hyperplasia of the lymph nodes who presented to NRITLD, Masih Daneshvari Hospital were retrospectively reviewed. After extracting the genomic DNA using phenol and chloroform, clonal analysis was performed using semi-nested PCR by using two primers: FR2 and FR3. PCR products were determined using 2 techniques of heteroduplex analysis, polyacrylamide gel and silver staining and the conventional method of agarose gel and ethidium bromide staining. Appearance of 1 or 2 bands in the desired location were considered as a sign of clonality., Results: Monoclonal gene rearrangement was observed in 62 out of 67 patients (92.5%) as one or two discrete bands appeared within 60-120 base pairs (bp) and 200-300 bp range. Of the mentioned patients, 53 cases (79.1%) had FR2 and 51 (76.1%) had FR3 rearrangement. Heteroduplex analysis along with silver nitrate staining detected 3 out of the remaining 5 cases of lymphoma to be monoclonal. These cases had been reported negative by the conventional technique. In total, 65 out of 67 patients (97%) showed monoclonal gene rearrangement using both the abovementioned techniques. All hyperplasia cases were polyclonal by this method., Conclusion: Our study showed that evaluation and detection of clonality using PCR, FR2 and FR3 primers along with heteroduplex analysis is a rapid sensitive technique for the diagnosis of malignant lymphomas.