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Trung NT, Quyen DT, Hoan NX, Giang DP, Trang TTH, Velavan TP, Bang MH, Song LH. Rapid, low cost and sensitive detection of Calreticulin mutations by a PCR based amplicon length differentiation assay for diagnosis of myeloproliferative neoplasms. BMC MEDICAL GENETICS 2019; 20:115. [PMID: 31248375 PMCID: PMC6598322 DOI: 10.1186/s12881-019-0819-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Calreticulin (CALR) gene mutations are currently recommended as biomarkers in diagnosis of patients with myeloproliferative neoplasms (MPN) with Jak2 V617F negative phenotype. Our aim was to establish a rapid, low cost and sensitive assay for identification of CALR gene mutations and to validate the diagnostic performance of the established assay in a patient cohort with different clinical MPN phenotypes. METHODS One hundred five Philadelphia-negative MPN patients, including polycythemia vera (PV), essential thrombocythaemia (ET), and primary myelofibrosis (PMF) were initially screened for JAK2 mutations by amplification-refractory mutation system (ARMS-PCR) methodology and were further subjected to detection of CALR gene mutations by our in-house assay, a PCR based amplicon length differentiation assay (PCR-ALDA). The PCR-ALDA methodology was compared with real time PCR and Sanger sequencing methods. Furthermore, the analytical sensitivity of the assay was established. RESULTS PCR - ALDA approach was able to detect and discriminate the pseudo-positive samples containing more than 1% CALR mutant alleles. CALR mutations were not detected in 63 Jak2 V617F positive cases in all three methods. In contrast, amongst 42 Jak2 V617F negative cases, both PCR-ALDA and Sanger sequencing coherently identified 12 CALR mutants compared to 10 CALR mutants detected by real-time PCR method. CONCLUSION PCR-ALDA can be utilized as an easy-to-use, rapid, low cost and sensitive tool in the detection of CALR mutations in Philadelphia-negative MPN patients.
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Affiliation(s)
- Ngo Tat Trung
- Centre for Genetic Consultation and Cancer Screening, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam.,Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam.,Department of Molecular Biology, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam
| | - Dao Thanh Quyen
- Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam.,Department of Molecular Biology, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam
| | - Nghiem Xuan Hoan
- Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam.,Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Dao Phuong Giang
- Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam.,Department of Molecular Biology, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam
| | - Tran Thi Huyen Trang
- Centre for Genetic Consultation and Cancer Screening, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam.,Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam.,Department of Molecular Biology, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam
| | - Thirumalaisamy P Velavan
- Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam.,Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Mai Hong Bang
- Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam.,Faculty of Gastroenterology, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese - German Center for Medical Research, 108 Institute of Clinical Medical and Pharmaceutical Sciences, No 1, Tran Hung Dao Street, Hai Ba Trung District, Hanoi, Vietnam. .,Faculty of Tropical and Infectious Diseases, 108 Institute of Clinical Medical and Pharmaceutical Sciences, Hanoi, Vietnam.
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Sultan S, Irfan SM, Khan SR. Somatic JAK-2 V617F Mutational Analysis in Polycythemia Rubra Vera: a Tertiary Care Center Experience. Asian Pac J Cancer Prev 2016; 17:1053-5. [PMID: 27039724 DOI: 10.7314/apjcp.2016.17.3.1053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polycythemia rubra vera (PV), being a primary polycythemia, is caused by neoplastic proliferation of erythroid, megakaryocytic and granulocytic lineages which result in panmyelosis. PV patients have a somatic acquired mutation in the Janus kinase (JAK2) pathway, rendering cell proliferation independent of the normal regulatory mechanisms that regulate erythropoiesis. The rational of this study was to determine the prevalence of the JAK-2 V617F mutation in Pakistani patients with PV. MATERIALS AND METHODS In this cross sectional study, 26 patients with PV were enrolled from January 2010 to December 2014. Patients were diagnosed based on WHO criteria for PV. All were screened for G-T point mutation (V617F) in the JAK2 gene on chromosome 9 by an allele specific PCR. RESULTS The mean age was 53.4±9.31 years (range 36-72) and the male to female ratio was 2:1. The frequency of JAK2 V617F positivity in our PV patients was found to be 92.3%. Overall 30.7% of patients were asymptomatic and remaining 69.3% presented with symptomatic disease. The mean hemoglobin was 18.1±1.9g/dl with the mean hematocrit of 55.6±8.3%. The mean total leukocyte count was 12.8±7.1x109/l and the platelet count was 511±341.9x109/l. A positive correlation of JAK2 V617F mutation was established with high TLC count (P=0.01). No correlation of JAK2 V617F could be established with age or gender (P>0.05). CONCLUSIONS The JAK2 V617F mutation frequency in our PV patients was similar to those reported internationally. Screening for the mutation in all suspected PV cases could be beneficial in differentiating patients with reactive and clonal erythrocytosis.
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Affiliation(s)
- Sadia Sultan
- Department of Hematology and Blood bank, Liaquat National Hospital and Medical College, Karachi Pakistan E-mail :
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Chhabra D, Sharma S, Kho AT, Gaedigk R, Vyhlidal CA, Leeder JS, Morrow J, Carey VJ, Weiss ST, Tantisira KG, DeMeo DL. Fetal lung and placental methylation is associated with in utero nicotine exposure. Epigenetics 2015; 9:1473-84. [PMID: 25482056 DOI: 10.4161/15592294.2014.971593] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In utero smoke exposure has been shown to have detrimental effects on lung function and to be associated with persistent wheezing and asthma in children. One potential mechanism of IUS effects could be alterations in DNA methylation, which may have life-long implications. The goal of this study was to examine the association between DNA methylation and nicotine exposure in fetal lung and placental tissue in early development; nicotine exposure in this analysis represents a likely surrogate for in-utero smoke. We performed an epigenome-wide analysis of DNA methylation in fetal lung tissue (n = 85, 41 smoke exposed (48%), 44 controls) and the corresponding placental tissue samples (n = 80, 39 smoke exposed (49%), 41 controls) using the Illumina HumanMethylation450 BeadChip array. Differential methylation analyses were conducted to evaluate the variation associated with nicotine exposure. The most significant CpG sites in the fetal lung analysis mapped to the PKP3 (P = 2.94 × 10(-03)), ANKRD33B (P = 3.12 × 10(-03)), CNTD2 (P = 4.9 × 10(-03)) and DPP10 (P = 5.43 × 10(-03)) genes. In the placental methylome, the most significant CpG sites mapped to the GTF2H2C and GTF2H2D genes (P = 2.87 × 10(-06) - 3.48 × 10(-05)). One hundred and one unique CpG sites with P-values < 0.05 were concordant between lung and placental tissue analyses. Gene Set Enrichment Analysis demonstrated enrichment of specific disorders, such as asthma and immune disorders. Our findings demonstrate an association between in utero nicotine exposure and variable DNA methylation in fetal lung and placental tissues, suggesting a role for DNA methylation variation in the fetal origins of chronic diseases.
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Affiliation(s)
- Divya Chhabra
- a Channing Division of Network Medicine; Brigham and Women's Hospital ; Boston , MA USA
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Cetin G, Ozkan T, Turgut S, Ali Cikrikcioglu M, Cem Ar M, Ayer M, Unlu A, Celik SR, Sekin Y, Karatoprak C. Evaluation of clinical and laboratory findings with JAK2 V617F mutation as an independent variable in essential thrombocytosis. Mol Biol Rep 2014; 41:6737-42. [DOI: 10.1007/s11033-014-3559-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 06/20/2014] [Indexed: 10/25/2022]
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