scholarly journals HBQ-India: an uncommon hemoglobin variant

2018 ◽  
Vol 6 (5) ◽  
pp. 1687
Author(s):  
Manjusha Dhawle ◽  
Ashok Methwani ◽  
Ashwini Tangde ◽  
Rajan Bindu
Keyword(s):  
Beta Thalassaemia ◽  
Arms Pcr ◽  
Sindh Province ◽  
High Prevalence ◽  
Different Types ◽  
Mutation System ◽  
Unknown Peak ◽  
Alpha Thalassaemia ◽  
Polymerase Chain ◽  
Hbq India

Background: HbQ-India is a rare alpha chain variant. It is an important member of the hemoglobin Q family molecularly characterized by replacement of aspartic acid by histidine. It usually presents in the heterozygous state. It becomes symptomatic only in the homozygous state and when present in association with other conditions like beta-thalassaemia, alpha thalassaemia, HbE and HbH. The Sindhi is one of the largest linguistic communities, migrated about 65 years back from the Sindh province of west Pakistan to India. They are a high-risk community for beta thalassaemia gene in India with a carrier frequency ranging from 5 to 12 % with a distinct regional variability.Methods: A total 343 cases were screened for hemoglobinopathies in Sindhi population. Detail history was taken from each patient and pertinent physical finding were noted. CBC, Peripheral smear and HPLC were performed. During screening we observed that few samples showed an unknown peak at a retention time of 4.7 min on HPLC and comparison with reference chromatograms indicated them to be HbQ India and it is confirmed by amplification restriction mutation system polymerase chain reaction (ARMS-PCR).Results: We found 13 cases, 12 cases of HbQ India and 1 case of HbQ-beta thalassaemia in Sindhi population of Aurangabad in Maharashtra.Conclusions: India is known as a country with a high prevalence of different types of hemoglobinopathy. Now a days HPLC, IEF, ARMS-PCR, DNA sequencing are the methods available for the diagnosis of the abnormal Hb like HbQ-lndia. HPLC is a cheaper alternative to ARMS-PCR in the detection of rare hemoglobinopathies.

scholarly journals Amplification Refractory Mutation System – Polymerase Chain Reaction for Rapid Detection of rpoB Gene Mutations in Mycobacterium tuberculosis

2017 ◽  
Vol 5 (1) ◽  
pp. 81-85 ◽  
Author(s):  
Hemanta Kumari Chaudhary ◽  
Mitesh Shrestha ◽  
Prakash Chaudhary ◽  
Bal Hari Poudel
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rpob Gene ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Arms Pcr ◽  
Mutation System ◽  
Mdr Tb ◽  
Total Dna ◽  
Polymerase Chain ◽  
Rifampin Resistance

Multidrug-resistant tuberculosis (MDR-TB) has become a serious worldwide threat including in Nepal. MDR-TB refers to the pathological condition whereby Mycobacterium tuberculosis becomes resistant to the first line of drug treatment i.e. rifampin and isoniazid. Resistance to rifampin (RIF) is mainly caused by the mutations in the rpoB gene which codes for the β-subunit of RNA polymerase. In this study, Amplification Refractory Mutation System – Polymerase Chain Reaction (ARMS – PCR) technique has been used to detect mutations in the rpoB gene of Mycobacterium tuberculosis. Total DNA samples of 34 phenotypic MDR-TB were subjected to ARMS – PCR using three different codon specific primers (516, 526 and 531). These three codons occupy large portion of total mutation responsible for rifampin resistance. Out of the total DNA samples, all were bearing mutation in at least one of the three codons mentioned. Of those bearing mutation, the highest number had mutation in codon 531 (97.05 %) followed by codon 516 (17.64 %) and finally in codon 526 (11.76%) respectively. Hence, ARMS – PCR may be used as an alternative diagnostic technique for detection of rifampin resistance in Mycobacterium tuberculosis strains, especially for a developing country like Nepal.Int. J. Appl. Sci. Biotechnol. Vol 5(1): 81-85

scholarly journals Prevalence of Adhesion and Regulation of Biofilm-Related Genes in Different Clones ofStaphylococcus aureus

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Salman Sahab Atshan ◽  
Mariana Nor Shamsudin ◽  
Zamberi Sekawi ◽  
Leslie Than Thian Lung ◽  
Rukman Awang Hamat ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Biofilm Formation ◽  
Clinical Information ◽  
Microtiter Plate ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Microtiter Plate Assay ◽  
High Prevalence ◽  
Different Types ◽  
Polymerase Chain

Clinical information about genotypically different clones of biofilm-producingStaphylococcus aureusis largely unknown. We examined whether different clones of methicillin-sensitive and methicillin-resistantS. aureus(MSSA and MRSA) differ with respect to staphylococcal microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) in biofilm formation. The study used 60 different types ofspaand determined the phenotypes, the prevalence of the 13 MSCRAMM, and biofilm genes for each clone. The current investigation was carried out using a modified Congo red agar (MCRA), a microtiter plate assay (MPA), polymerase chain reaction (PCR), and reverse transcriptase polymerase chain reaction (RT-PCR). Clones belonging to the samespatype were found to have similar properties in adheringto thepolystyrene microtiter plate surface. However, their ability to produce slime on MCRA medium was different. PCR experiments showed that 60 clones of MSSA and MRSA were positive for 5 genes (out of 9 MSCRAMM genes).icaADBCgenes were found to be present in all the 60 clones tested indicating a high prevalence, and these genes were equally distributed among the clones associated with MSSA and those with MRSA. The prevalence of other MSCRAMM genes among MSSA and MRSA clones was found to be variable. MRSA and MSSA gene expression (MSCRAMM andicaADBC) was confirmed by RT-PCR.

scholarly journals A Tetra-Primer Amplification Refractory Mutation System–Polymerase Chain Reaction (T-ARMS-PCR) for Genotyping of rs8099917 & rs12979860 IL28B Polymorphisms and Its Correlation of Various Variables in Iranian HCV Patients

2020 ◽  
pp. 31-41
Author(s):  
Ali Bahari ◽  
Mohammad Hashemi ◽  
Gholam Reza Bahari ◽  
Tahereh Fakharian ◽  
Sina Gerayli ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Load ◽  
Hepatitis C ◽  
Gene Polymorphisms ◽  
Baseline Viral Load ◽  
Amplification Refractory Mutation System ◽  
Chain Reaction ◽  
Arms Pcr ◽  
Mutation System ◽  
Polymerase Chain

Background: Selecting patients for new direct acting antiviral treatment of HCV has prompted a conflicting matter worldwide because of its high cost and limited availability. Genotyping of IL28B polymorphisms will aid clinical decision making for identifying priorities of urgent treatment in resource-limited countries. Objectives: The aim of the present study was to design a simple tetra-primer amplification refractory mutation system–polymerase chain reaction (T-ARMS-PCR) for genotyping of the rs8099917 and rs12979860 IL28B gene polymorphisms. Furthermore, we identify the correlation of variables such as gender, serum ALT level, histology of liver and baseline viral load with these polymorphisms. Patients and Methods: We efficiently designed a T-ARMS-PCR for detection of rs12979860 and rs8099917 IL28B gene polymorphisms. Using this method, we genotyped 148 hepatitis C patients. To ensure T-ARMS genotyping quality, we, regenotyped samples with the PCR- sequencing method. Results: Results of genotyping of rs12979860 and rs8099917 by T-ARMS PCR method were 100% concordant with the sequencing results. Among these 148 patients with chronic hepatitis C, the frequency of the rs12979860 CT, TT and CC genotypes was 72.3%, 14.2% and 13.5%, respectively and the frequency of the rs8099917 TT, GT and GG genotypes was 58.1%, 38.5% and 3.4%. Low frequency (2.7%) of association of two unfavourable homozygous genotypes (TT rs12979860 / GG rs809917) as well as 56.7% of association of 3 or 4 favorable alleles could explain good response of Iranians to HCV treatment with interferon-based regimens. About correlation of polymorphisms with different variables, only high viral load showed a statistically significant correlation to unfavorable genotype of TT rs12979860 ( p value = 0/05 ) and there was no correlation of  serum ALT level, gender and  histology of liver to IL28B genotypes. Conclusions: We report that rs8099917 polymorphisms could predict outcomes better than rs12979860 in Iranian HCV patients.

scholarly journals PCSK9 Gene Polymorphisms Associated With the Risk of Myocardial Infarction in Iranian Patients

2021 ◽  
Vol 6 (2) ◽  
pp. 57-63
Author(s):  
Farshad Namordizadeh ◽  
Mahboobeh Nasiri
Keyword(s):  
Myocardial Infarction ◽  
Gene Polymorphisms ◽  
Prognostic Markers ◽  
Regulatory Protein ◽  
Amplification Refractory Mutation System ◽  
Pcsk9 Gene ◽  
Arms Pcr ◽  
Increased Risk ◽  
Mutation System ◽  
Polymerase Chain

Introduction: Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a key regulatory protein in lipid metabolism and a candidate gene in the etiology of cardiovascular diseases. The present study aimed to evaluate the prevalence and significance of PCSK9 rs505151 and rs11591147 variants with myocardial infarction (MI) risk in the Iranian population. Patients and Methods: The frequency of the PCSK9 rs505151 and rs11591147 variants were compared between 600 cases of MI and 600 healthy age- and sex-matched individuals. Tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS PCR) was used for rs505151, and amplification refractory mutation system-polymerase chain (ARMS-PCR) was utilized to detect the rs11591147 polymorphism. Finally, SPSS and SHEsis software were applied for data analysis. Results: Carriers of the GG genotype of rs505151 polymorphism (OR: 1.57, 95% CI: 1.05–2.35, P = 0.02; age-adjusted; OR: 1.54, 95% CI: 1.03–2.32, P = 0.03) and at least one G-allele including GG+AG vs. AA (OR: 1.54, 95% CI: 1.04–2.28, P = 0.03; age-adjusted; OR: 1.51, 95% CI: 1.01–2.24, P = 0.04) have an increased risk of MI. No association between PCSK9 rs505151 alleles and MI risk was observed. The ratio of individuals with the rs11591147GT variant was higher in healthy individuals vs. patients with MI (48.6% vs. 41.7%), indicating a reduced risk of developing MI (OR: 0.75; 95% CI: 0.59–0.95; P = 0.01; age-adjusted; OR: 0.74; 95% CI: 0.58–0.95; P = 0.01). The carriers of at least one T allele (TT+GT vs. GG) (OR: 0.78; 95% CI: 0.62–0.98; P = 0.03; age-adjusted; OR: 0.78; 95% CI: 0.62–0.98; P = 0.03) showed a significant reduction in MI risk. The allelic frequencies at this polymorphic site did not differ between MI patients and healthy counterparts. No association was found between the haplotypes constructed from the alleles of these two polymorphisms. Conclusion: Our study provides the first evidence that PCSK9 gene polymorphisms may serve as independent prognostic markers for MI patients in Iran.

Evaluation of a new efficient procedure for single-nucleotide polymorphism genotyping: tetra-primer amplification refractory mutation system-polymerase chain reaction

2004 ◽  
Vol 42 (1) ◽  
Author(s):  
Naoko Okayama ◽  
Kozue Fujimura ◽  
Junji Nakamura ◽  
Yutaka Suehiro ◽  
Yuichiro Hamanaka ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphism ◽  
Snp Genotyping ◽  
Amplification Refractory Mutation System ◽  
Nucleotide Polymorphism ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Arms Pcr ◽  
Mutation System ◽  
Polymerase Chain

AbstractTetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) is a new efficient method for single-nucleotide polymorphism (SNP) genotyping. To determine the optimal conditions for ARMS-PCR we attempted to genotype ten SNPs. DNA was extracted from the peripheral blood of 168 unrelated healthy Japanese volunteers. Two problems inhibited uniform efficiency of the amplification of three bands. The first problem was the lower amplification efficiency of the shorter and allele-specific products compared with the largest product. This phenomenon was overcome by increasing the relative concentration of the inner primers. The second problem was non-specific amplification of the shorter products. To reduce the amplification of these nonspecific bands, adjusting any one of the following PCR conditions was effective: i) reducing the ratio of the inner primer concentration relative to that of the outer primers; ii) increasing the annealing temperature for the initial 5–10 cycles; iii) hot start PCR. With these procedures all ten of the SNPs were successfully genotyped. Our present data may be useful in the further application of tetra-primer ARMS-PCR to SNP genotyping.

scholarly journals Mutation Pattern in Beta Thalassaemia Trait Population: A Basis for Prenatal Diagnosis

2018 ◽  
Vol 44 (2) ◽  
pp. 65-70 ◽  
Author(s):  
Bilquis Banu ◽  
Waqar Ahmed Khan ◽  
Md. Selimuzzaman ◽  
Golam Sarwardi ◽  
Salma Sadiya
Keyword(s):  
Prenatal Diagnosis ◽  
Amplification Refractory Mutation System ◽  
Specific Primers ◽  
Rare Mutation ◽  
Beta Thalassaemia ◽  
Mutation System ◽  
Thalassaemia Trait ◽  
Allele Specific ◽  
Mutation Pattern ◽  
Polymerase Chain

A total of 100 Bangladeshi beta thalassaemia carrier subjects were analysed by allele specific primers using Amplification Refractory Mutation System – Polymerase Chain Reaction.  Among these, four common mutations were found in 90 cases (90.0%), five less common mutations in 9 cases (9.0%) and a rare mutation in 1 case (1.0%). Among the four common mutations, IVS1-5 (G-C) was the most common beta thalassaemia mutation and found in 63.0% cases, followed by Cd 30 (G-C) in 18.0%, Fr 8/9 (+G) in 5.0% and Fr 41/42 (-TTCT) in 4.0% respectively. Among the five less common mutations, Cd16 (-C) was found in 3.0%, -90 (C-T) and IVS1-130 (G-C) were seen in 2.0% each and remaining Cd15 (-T) and Cd15 (G-A) were detected in 1.0% each. The rare mutation was -29 (A-G), observed in one case (1.0%). With the application of this knowledge, it will help us for prenatal diagnosis and genetic counselling in Bangladesh for prevention of the disease.

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