Infectious Diseases
Mohammad Vasei; Elham Jafari; Vahid Falah Azad; Moeinadin Safavi; Maryam Sotoudeh
Abstract
From the beginning of the COVID-19 epidemic, clinical laboratories around the world have been involved with tests for detection of SARS-CoV-2. Currently, RT-PCR (real-time reverse transcription polymerase chain reaction assay) is the gold standard for identifying the virus. Many factors are involved ...
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From the beginning of the COVID-19 epidemic, clinical laboratories around the world have been involved with tests for detection of SARS-CoV-2. Currently, RT-PCR (real-time reverse transcription polymerase chain reaction assay) is the gold standard for identifying the virus. Many factors are involved in achieving the highest accuracy in this test, including parameters related to the pre-analysis stage. Having instructions on the type of sample, how to take the sample, and its storage and transportation help control the interfering factors at this stage. Studies have shown that pre-analytical factors might be the cause of the high SARS-CoV-2 test false-negative rates. Also, the safety of personnel in molecular laboratories is of utmost importance, and it requires strict guidelines to ensure the safety of exposed individuals and prevent the virus from spreading. Since the onset of the outbreak, various instructions and guidelines have been developed in this field by the institutions and the Ministry of Health of each country; these guidelines are seriously in need of integration and operation. In this study, we try to collect all the information and research done from the beginning of this pandemic in December 2019- August 2022 concerning biosafety and protective measures, sample types, sampling methods, container and storage solutions, sampling equipment, and sample storage and transportation for molecular testing of SARS-CoV-2.
Hematopathology
Moeinadin Safavi; Ahmad Monabati; Akbar Safaie; Maryam Mirtalebi; Masoumeh Faghih
Abstract
Background: This study was conducted to evaluate the frequency of JAK2, CALR and MPL mutations in with BCR-ABL myeloproliferative neoplasms and their association with demographic data and hematologic parameters in a referral center, in the Middle East. Methods: Seventy-one patients with BCR-ABL negative ...
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Background: This study was conducted to evaluate the frequency of JAK2, CALR and MPL mutations in with BCR-ABL myeloproliferative neoplasms and their association with demographic data and hematologic parameters in a referral center, in the Middle East. Methods: Seventy-one patients with BCR-ABL negative myeloproliferative neoplasms were evaluated for JAK2 V617F, CALR type 1, type 2, and MPL by allele-specific PCR and conventional PCR from 2018 to 2019. Results: Twenty three patients were categorized as polycythemia vera and demonstrated JAK2 V617F in 91.3 % of these cases. Thirty-eight patients were classified as essential thrombocythemia and showed JAK2 V617F in 52.6%, CALR type 1 in 18.4%, CALR type 2 in 7.9% and no mutation in 21.1%. Seven patients were recognized as primary myelofibrosis and exhibited JAK2 V617F mutation in 57.1%, CALR type 1 in 14.3 %, CALR type 2 in 14.3% and no mutation in 14.3%. Three patients were diagnosed as MPN, unclassifiable and revealed JAK2 V617F mutation in 33.3% and no mutation in 66.6%.The age (59.15±13.10) and neutrophil percent (70.78±10.14) were higher in patients with JAK2 mutation compared to other mutations (p=0.000, and p=0.03). Platelet count was significantly higher in patients with CALR type 1 mutation (1240400± 402053) (p=0.000). Conclusion: JAK2 V617F was was associated with patients’ higher age and higher neutrophil count in CBC. CALR mutation had an association with higher platelet count. No MPL mutation was found in this study and it seems that its frequency is lower than what is expected in this region.
Molecular Pathology
Maryam Sotoudeh Anvari; Atoosa Gharib; Maryam Abolhasani; Aileen Azari-Yaam; Farzaneh Hossieni Gharalari; Moeinadin Safavi; Ali Zare-Mirzaie; Mohammad Vasei
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors which ...
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Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors which take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
Molecular Pathology
Freidoon Solhjoo; Akbar Safaie; Ahmad Monabati; Maral Mokhtari; Moeinadin Safavi
Volume 13, Issue 4 , October 2018, , Pages 438-446
Abstract
Background and Objective: Identification of cytogenetic and molecular changes plays an important role in acute myeloid leukemia (AML) patients. Thus, they are used in classification, prognosis and treatment of the disease. The CD123 expression and FLT3 gene mutations are also the variations that may ...
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Background and Objective: Identification of cytogenetic and molecular changes plays an important role in acute myeloid leukemia (AML) patients. Thus, they are used in classification, prognosis and treatment of the disease. The CD123 expression and FLT3 gene mutations are also the variations that may assist in prognosis and treatment of patients with AML.Methods: This study was performed on 76 patients as new cases of AML. The correlation between CD123 immunohistochemical (IHC) expression and FLT3 gene mutations with each other as well as morphological, immunophenotypical and cytogenetic factors was studied.Results: The results represented the CD123 IHC expression in 55.3% and FLT3 gene mutations in 28.9% of cases. We found that 81.3% of patients who had FLT3/ITD gene mutations revealed IHC of CD123 expression (P=0.019). The CD123 expression against FLT3 was also correlated with monocytic differentiation in bone marrow blasts (P=0.031). There were significant correlations between IHC expression of CD123 and FLT3/ITD mutations with a high percentage of aspirated bone marrow blasts (P=0.01 and P=0.006, respectively) as well as the lack of CD34 expression in bone marrow blasts (P=0.007 and P=0.021, respectively).Conclusion: The CD123 IHC positive AMLs were correlated with certain pathologic features, some of which can be similar with correlations of background mutation of FLT3/ITD; According to the negative predictive value (NPV), 88.2% of CD123 IHC showed FLT3 gene mutation. In addition to its use in targeted therapy, it could be a marker to decide what molecular tests to use in the next steps.
Katayoun Ziari; Mojgan Sanjari; Moeinadin Safavi
Abstract
Background & objective: papillary thyroid cancer is the most common cancer of thyroid accounting for 75%-85% of all thyroid malignancies. Recently, β-catenin has been determined to play a role in clinical course of human epithelial cancers. This study was designed to reveal the association of ...
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Background & objective: papillary thyroid cancer is the most common cancer of thyroid accounting for 75%-85% of all thyroid malignancies. Recently, β-catenin has been determined to play a role in clinical course of human epithelial cancers. This study was designed to reveal the association of β-catenin marker and papillary thyroid carcinoma behavior. Methods: 63 paraffin blocks of papillary thyroid carcinoma were stained with ready to use monoclonal β-catenin antibody according to manufacturer’s instructions. Memberanous, cytoplasmic and nuclear staining was scored according to intensity of immunoreactivity. β-catenin immunostaining association with clinical parameters like number of recurrences and cumulative dose of radioiodine therapy were analyzed using SPSS version 15. Histopathologic parameters like tumor stage, grade, capsular invasion, lymphovascular invasion, lymph node involvement, distant metastasis and other variables were also evaluated for association with β-catenin immunoreactivity Results: 77.8% of papillay thyroid carcinoma were well differentiated and the remaining were poorly differentiated. Loss of β-catenin membrane immunostaining depicted correlation with number of recurrences (p=0.023% , Pearson correlation= -0.285). Its loss of memberanous staining correlated similarly with cumulative dose of radioiodine (p= 0.046, Pearson correlation = -0.253). Loss of membranous β-catenin was significantly associated with some histopathologic findings like nodal involvement (p<0.001), distant metastasis (p=0.003) and tumor dedifferentiation (p< 0.001). Conclusion: Loss of β-catenin membranous staining and its cytoplasmic accumulation were associated with aggressive clinicopathologic behavior. The exact effect of radioiodine exposure on β-catenin pathway remained to be determined in future.
Moeinadin Safavi; Jahanbanoo Shahryari; Mohammadmehdi Moeini Aghtaei; Hossein Nikpour
Volume 11, Issue 3 , July 2016, , Pages 255-260
Abstract
Desmoplastic small round cell tumor (DSCRT) is a rare variant of sarcoma with a highly aggressive behavior. It usually affects abdominal cavity and has a male predominance. Its correct diagnosis and treatment is sophisticated and requires an experienced multidisciplinary team. Hereby we present a 25 ...
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Desmoplastic small round cell tumor (DSCRT) is a rare variant of sarcoma with a highly aggressive behavior. It usually affects abdominal cavity and has a male predominance. Its correct diagnosis and treatment is sophisticated and requires an experienced multidisciplinary team. Hereby we present a 25 yrold man from Kerman Province in 2013 with abdominal mass and ascites who underwent sonograghy guided percutaneous needle biopsy which was misleading and inconclusive for diagnosis. Thus an open biopsy was fulfilled which revealed solid nests of small round cells with hyperchromatic nuclei and clear cytoplasm surrounded by a desmoplastic stroma suggestive for DSCRT. The diagnosis was confirmed by positive immunohitochemical reaction for cytokeratin, desmin and neuron specific enolase(NSE).Ultimately the patient underwent chemotherapy on the basis of P6 protocol without surgical debulking.Diagnosis and treatment of DSCRT could be a dilemma due to its rarity, various clinicopathologic mimickers and lack of a consensus about its management.
Moeinadin Safavi; Shahriar Dabiri
Volume 11, Issue 3 , July 2016, , Pages 296-297
Abstract
Hemangiomas are considered as vascular malformations which are categorized by the type of vascular channel to capillary, cavernous, venous or arteriovenous(1). Their usual locations are soft tissue , cutaneous or subcutaneous tissue and bone especially vertebra(2).However, intradural extramedullary hemangiomas ...
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Hemangiomas are considered as vascular malformations which are categorized by the type of vascular channel to capillary, cavernous, venous or arteriovenous(1). Their usual locations are soft tissue , cutaneous or subcutaneous tissue and bone especially vertebra(2).However, intradural extramedullary hemangiomas are rare and most of them fall in cavernous type category. Hereby, authors report a woman with spinal intradural extramedullary capillary hemangioma which is exceedingly rare.
Moeinadin Safavi; Shahriar Dabiri
Volume 11, Issue 2 , April 2016, , Pages 186-188
Abstract
Leishmaniasis include several clinical manifestations, mostly cutaneous, visceral and mucosal (1, 2). Various species can lead to diverse clinical presentations. Thus species identification contribute to proper management (3). Localized Leishmania Lymphadenitis (LLL) is a distinct entity in clinicopathologic ...
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Leishmaniasis include several clinical manifestations, mostly cutaneous, visceral and mucosal (1, 2). Various species can lead to diverse clinical presentations. Thus species identification contribute to proper management (3). Localized Leishmania Lymphadenitis (LLL) is a distinct entity in clinicopathologic field presenting with isolated lymphadenitis and possible cocomitant cutaneous lesion in the absence of systemic visceral involvement (4). Species identification has been acceptable by conventional microscopic evaluation, serologic methods such as isoenzyme and monoclonal antibody detection and particularly PCR. However, definite identification and confirmation of parasite without gene sequencing have always been doubted (5).
Moeinadin Safavi; Shahriar dabiri; Nahid Monsefi
Volume 11, Issue 1 , January 2016, , Pages 85-87
