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Objective@#To explore the genetic basis for a Chinese pedigree affected with pachyonychia congenita (PC).@*Methods@#With informed consent obtained, peripheral blood samples were taken from the pedigree. Genomic DNA was extracted with a phenol/chloroform method. Based on the clinical manifestation of the patients, candidate genes for PC were selected. Potential mutation was screened by PCR and Sanger sequencing. Suspected mutation was verified in other family members by PCR-high resolution melting (HRM) analysis. Haplotype analysis using microsatellite markers was also carried out to determine the founder of the mutation.@*Results@#A heterozygous c. 275A>G (Asn92Ser) mutation was discovered in exon 1 of the KRT17 gene in the proband. PCR-HRM analysis showed that all affected members were heterozygous carriers of the mutation. The same mutation was found in none of the unaffected members. Haplotype analysis and sequencing indicated the mother of the proband to be the founder.@*Conclusion@#The c. 275A>G (Asn92Ser) mutation of the KRT17 gene probably underlies the disease in this pedigree. Above finding has facilitated genetic counseling and prenatal diagnosis for this pedigree.
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Objective: To detect and identify filarial parasites in dried blood spots (DBS) collected from domestic cats using high resolution melting real-time PCR (HRM RT-PCR). Methods: A total of 208 DBS were collected from domestic cats in a brugian filariasis endemic areas in Surat Thani Province, southern Thailand. Microfilariae were found in 9 blood slides using Giemsa-stained thick blood film. The extracted DNA from blood spot volumes of 10 and 20 μL DBS with positive filarial parasites in cats were performed using HRM RT-PCR method. The primers were designed based on the partial mitochondrial 12S rRNA gene for identifying Brugia malayi, Brugia pahangi, Dirofilaria immitis. All purified samples were then detected. Results: Using different volumes of 10 μL and 20 μL DBS could easily distinguish filarial parasites and showed similar results. PCR amplicons of Brugia malayi, Brugia pahangi and Dirofilaria immitis were determined at melting peak (temperature) of 75.70 77.46 and 73.56 respectively. All 9 positive DBS samples showed positive Brugia pahangi and similar nucleotide sequences. Conclusions: This HRM RT-PCR method is able to diagnose, identify and discriminate filarial parasites collected from DBS, which is simple and inexpensive compared with other probe-based genotyping methods. Furthermore, this method is useful to survey, prevent and control filariasis.
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Objective:To detect and identify filarial parasites in dried blood spots (DBS) collected from domestic cats using high resolution melting real-time PCR (HRM RT-PCR).Methods:A total of 208 DBS were collected from domestic cats in a brugian filariasis endemic areas in Surat Thani Province, southern Thailand. Microfilariae were found in 9 blood slides using Giemsa-stained thick blood film. The extracted DNA from blood spot volumes of 10 and 20 μL DBS with positive filarial parasites in cats were performed using HRM RT-PCR method. The primers were designed based on the partial mitochondrial 12S rRNA gene for identifying Brugia malayi, Brugia pahangi, Dirofilaria immitis. All purified samples were then detected.Results:Using different volumes of 10 μL and 20 μL DBS could easily distinguish filarial parasites and showed similar results. PCR amplicons of Brugia malayi, Brugia pahangi and Dirofilaria immitis were determined at melting peak (temperature) of 75.70 77.46 and 73.56 respectively. All 9 positive DBS samples showed positive Brugia pahangi and similar nucleotide sequences.Conclusions:This HRM RT-PCR method is able to diagnose, identify and discriminate filarial parasites collected from DBS, which is simple and inexpensive compared with other probe-based genotyping methods. Furthermore, this method is useful to survey, prevent and control filariasis.
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High-resolution melting (HRM) analysis is a versatile method for variant scanning and genotyping. It involves amplification of the target in the presence of a saturation dye by the polymerase chain reaction (PCR). HRM analysis can be performed in one closed-tube, which does not require additional post-PCR separations and greatly reduces the possibility of contamination. HRM is faster, simpler, and less expensive than alternative approaches requiring labeled probes. Considering the many advantages of HRM analysis, many researchers have tried to apply this method to forensic research. This paper intends to summarize the principle, technical characteristics, limitations and application of HRM analysis in forensic science.
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Objective To identify the single nucleotide polymorphism (SNP) of the gene of TNIP1 using high resolution melting (HRM) analysis with unlabeled probe,and funther analyse the association with systemic lupus erythematosuscsle.Methods 297 patients that fulfilled the American College of Rheumatology criteria for SLE and 351 ethnically matched healthy controls were recruited from Shenzhen Hospital of Peking University.The association of TNIP1 SNP rs7708392 (G/C) was determined by high resolution melting (HRM) analysis with unlabeled probe in SLE patients and healthy controls.Results HRMA with unlabeled probe successfully distinguished all genotypes.Genotype frequencies of GG,GC and CC among SLE patients were 36.0％,51.5％ and 12.5％,respectively,while the frequencies among healthy control were 32.5％,46.7％ and 20.8％.Statistically significant differences were observed in both genotype frequencies for rs7708392 in the SLE patients as compared with the controls.Minor allele (C) of rs7708392 (P=0.031,OR 0.78,95％ CI 0.63～0.98) was found to be protective against SLE.The association of SNP rs7708392 with the diagnostic criteria of SLE was also examined.Minor allele (C) exerts protective effect on the incidence of arthritis (P=0.013,OR=0.65,95 ％ CI=0.47 ～ 0.92) and abnormalities of antinuclear antibody (P =0.022,OR =0.68,95 ％ CI =0.49 ～ 0.95).TNIP1 SNPs were irrelevant to other diagnostic criteria of SLE.Conclusion Polymorphisms of rs7708392 in TNIP1 gene were associated with disease risk,as well as arthritis and autoantibody production,of systemic lupus erythematosus in Chinese population.
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Objective To study the SRSF2 mutations in acute myeloid leukemia (AML) patients by using high-resolution melting analysis (HRMA). Methods PCR-HRMA analysis was performed to screen SRSF2 mutations in 140 cases with AML, and the direct DNA sequencing was used to confirm the HRMA results. Results Five percent (7/140) of AML patients were found with heterozygous SRSF2 mutations, including one case of P95R mutation, two case of P95L mutation, and four cases of P95H mutation, the above mutations were confirmed by direct DNA sequencing. The maximal sensitivity of HRMA in detecting SRSF2 mutation was close to 10%. There were no difference in gender, age and blood parameters among cases with or without SRSF2 mutations (P > 0.05). The overall survival (OS) of patients with SRSF2 mutations was inferior to those without SRSF2 mutations in AML patients (P=0.016). Conclusions HRMA analysis was a convenient, rapid, specific, high-throughput technique for scanning of SRSF2 gene mutations in AML patients. SRSF2 mutation may predict the adverse prognosis in AML patients.
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Objective The K-ras gene plays a major role in the development , progression, and drug selection for the target treatment of colorectal cancer .The aim of this study was to evaluate the feasibility of detecting K-ras mutation in colorectal cancer by high-resolution melting ( HRM) analysis and to investigate the relationship between K-ras mutation and the clinicopathological parame-ters of colorectal cancer. Methods We collected the tissue samples of colorectal cancer from 179 patients, detected the mutations in codons 12 and 13 of the K-ras gene, and analyzed the relationship between K-ras mutation and the clinicopathological parameters of the patients. Results In the 179 cases of colorectal cancer, K-ras mutation was found in 77 (43.02%), significantly higher in those aged ≥60 years than in those aged <60 years (55.17% vs 33.70%, P<0.05).Multivariate logistic regression analysis showed a significant influence of age on K-ras mutation (OR=1.506, 95%CI:1.028-2.011, P<0.05). Conclusion HRM analysis is a rapid, sensitive, and inexpensive diagnostic tool for the detection of K-ras mutation, and K-ras mutation is associated with the age of colorectal cancer patients .
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Objective To establish a high resolution melting based method for the rapid identifica-tion of functional class 2 integron.Methods Nighty-nine non-repetitive Proteus spp.strains positive for genes encoding class 2 integrase were isolated from August, 2011 to August, 2012.The genomic DNAs were extracted and used as templates to amplify 60 base pair fragments containing the mutated point in class 2 in-tegrase gene by PCR.The high resolution melting analysis was conducted to identify the functional class 2 in-tegrons that were further compared by sequence analysis.Results There were remarkable differences with the high resolution melting curves between the functional class 2 integrons and the ordinary class 2 integrons. The results of high resolution melting analysis were consistent with those by using sequence analysis.Con-clusion High resolution melting analysis could be used for the rapid and accurate identification of functional class 2 integron.
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Human schistosomiasis caused by Schistosoma japonicum and Schistosoma mekongi is a chronic and debilitating helminthic disease still prevalent in several countries of Asia. Due to morphological similarities of cercariae and eggs of these 2 species, microscopic differentiation is difficult. High resolution melting (HRM) real-time PCR is developed as an alternative tool for the detection and differentiation of these 2 species. A primer pair was designed for targeting the 18S ribosomal RNA gene to generate PCR products of 156 base pairs for both species. The melting points of S. japonicum and S. mekongi PCR products were 84.5+/-0.07degrees C and 85.7+/-0.07degrees C, respectively. The method permits amplification from a single cercaria or an egg. The HRM real-time PCR is a rapid and simple tool for differentiation of S. japonicum and S. mekongi in the intermediate and final hosts.
Subject(s)
Animals , Mice , DNA Primers/genetics , Parasitology/methods , RNA, Ribosomal, 18S/genetics , Real-Time Polymerase Chain Reaction/methods , Schistosoma/classification , Snails , Time Factors , Transition TemperatureABSTRACT
BACKGROUND: Accurate typing of Duffy blood group is important because anti-Duffy antibodies cause hemolytic transfusion reaction and hemolytic disease of the newborn. The aim of this study was to evaluate a new genotyping method using high resolution melting (HRM) analysis, a rapid and inexpensive approach for high-throughput Duffy genotyping. METHODS: A total of 20 unrelated Korean blood samples were obtained and an African-black sample was used for GATA control. Phenotyping was performed by hemagglutination (DiaMed AG, Switzerland). GATA and FYA/B PCR products were obtained by PCR-restriction fragment length polymorphism (RFLP) using Taq DNA polymerase (Promega, WI) and enzymes BanI and StyI (New England Biolab, UK). For HRM, PCR amplification was performed using LightCycler 480 ResoLight Dye (Roche, USA) and Lightcycer 480 (Roche, USA). RESULTS: Phenotyping and genotyping data using PCR-RFLP and HRM analysis were compared. Different types of HRM curves were obtained according to genotypes, FYA/FYA, FYB/FYB, and FYA/FYB, and to GATA mutations, homozygote FYB-33T (T/T), heterozygote FYB-33T/33C (T/C), and homozygote FYB-33C (C/C). Phenotypes 18 Fy(a+b-), 1 Fy(a+b+), 1 Fy(a-b+), and 1 Fy(a-b-) showed complete concordance with genotyping methods. Fy(a-b-) sample was found to be a FYB-33C homozygote by both genotyping methods. CONCLUSION: Phenotyping and genotyping showed concordant results and both genotyping methods using PCR-RFLP and HRM analysis showed good agreement in finding mutation in GATA and FY gene coding regions. HRM analysis is suitable and reliable for high-throughput screening for Duffy genotyping.
Subject(s)
Humans , Infant, Newborn , Antibodies , Blood Group Antigens , Blood Group Incompatibility , Clinical Coding , England , Freezing , Genotype , Hemagglutination , Heterozygote , Homozygote , Mass Screening , Phenotype , Polymerase Chain Reaction , Taq PolymeraseABSTRACT
Opisthorchis viverrini and Clonorchis sinensis are parasites known to be carcinogenic and causative agents of cholangiocarcinoma in Asia. The standard method for diagnosis for those parasite infections is stool examination to detect parasite eggs. However, the method has low sensitivity, and eggs of O. viverrini and C. sinensis are difficult to distinguish from each other and from those of some other trematodes. Here, we report a multiplex real-time PCR coupled with high resolution melting (HRM) analysis for the differentiation of O. viverrini and C. sinensis eggs in fecal samples. Using 2 pairs of species-specific primers, DNA sequences from a portion of the mitochondrial NADH dehydrogenase subunit 2 (nad 2) gene, were amplified to generate 209 and 165 bp products for O. viverrini and C. sinensis, respectively. The distinct characteristics of HRM patterns were analyzed, and the melting temperatures peaked at 82.4+/-0.09degrees C and 85.9+/-0.08degrees C for O. viverrini and C. sinensis, respectively. This technique was able to detect as few as 1 egg of O. viverrini and 2 eggs of C. sinensis in a 150 mg fecal sample, which is equivalent to 7 and 14 eggs per gram of feces, respectively. The method is species-specific, rapid, simple, and does not require fluorescent probes or post-PCR processing for discrimination of eggs of the 2 species. It offers a new tool for differentiation and detection of Asian liver fluke infections in stool specimens.
Subject(s)
Animals , Humans , Asia , Clonorchis sinensis/classification , Feces/parasitology , Multiplex Polymerase Chain Reaction/methods , NADH Dehydrogenase/genetics , Opisthorchis/classification , Parasitology/methods , Real-Time Polymerase Chain Reaction/methods , Sensitivity and Specificity , Transition Temperature , ZygoteABSTRACT
BACKGROUND: Prevention and control of thalassemia requires simple, rapid, and accurate screening tests for carrier couples who are at risk of conceiving fetuses with severe thalassemia. METHODS: Single-tube multiplex real-time PCR with SYBR Green1 and high-resolution melting (HRM) analysis were used for the identification of alpha-thalassemia-1 Southeast Asian (SEA) and Thai type deletions and beta-thalassemia 3.5-kb gene deletion. The results were compared with those obtained using conventional gap-PCR. DNA samples were derived from 28 normal individuals, 11 individuals with alpha-thalassemia-1 SEA type deletion, 2 with alpha-thalassemia-1 Thai type deletion, and 2 with heterozygous beta-thalassemia 3.5-kb gene deletion. RESULTS: HRM analysis indicated that the amplified fragments from alpha-thalassemia-1 SEA type deletion, alpha-thalassemia-1 Thai type deletion, beta-thalassemia 3.5-kb gene deletion, and the wild-type beta-globin gene had specific peak heights at mean melting temperature (Tm) values of 86.89degrees C, 85.66degrees C, 77.24degrees C, and 74.92degrees C, respectively. The results obtained using single-tube multiplex real-time PCR with SYBR Green1 and HRM analysis showed 100% consistency with those obtained using conventional gap-PCR. CONCLUSIONS: Single-tube multiplex real-time PCR with SYBR Green1 and HRM analysis is a potential alternative for routine clinical screening of the common types of alpha- and beta-thalassemia large gene deletions, since it is simple, cost-effective, and highly accurate.
Subject(s)
Humans , Asia, Southeastern , Asian People/genetics , Gene Deletion , Genotype , Organic Chemicals/chemistry , Phase Transition , Polymerase Chain Reaction/methods , Reagent Kits, Diagnostic , Thailand , Transition Temperature , alpha-Thalassemia/diagnosis , beta-Thalassemia/diagnosisABSTRACT
BACKGROUND: Prevention and control of thalassemia requires simple, rapid, and accurate screening tests for carrier couples who are at risk of conceiving fetuses with severe thalassemia. METHODS: Single-tube multiplex real-time PCR with SYBR Green1 and high-resolution melting (HRM) analysis were used for the identification of alpha-thalassemia-1 Southeast Asian (SEA) and Thai type deletions and beta-thalassemia 3.5-kb gene deletion. The results were compared with those obtained using conventional gap-PCR. DNA samples were derived from 28 normal individuals, 11 individuals with alpha-thalassemia-1 SEA type deletion, 2 with alpha-thalassemia-1 Thai type deletion, and 2 with heterozygous beta-thalassemia 3.5-kb gene deletion. RESULTS: HRM analysis indicated that the amplified fragments from alpha-thalassemia-1 SEA type deletion, alpha-thalassemia-1 Thai type deletion, beta-thalassemia 3.5-kb gene deletion, and the wild-type beta-globin gene had specific peak heights at mean melting temperature (Tm) values of 86.89degrees C, 85.66degrees C, 77.24degrees C, and 74.92degrees C, respectively. The results obtained using single-tube multiplex real-time PCR with SYBR Green1 and HRM analysis showed 100% consistency with those obtained using conventional gap-PCR. CONCLUSIONS: Single-tube multiplex real-time PCR with SYBR Green1 and HRM analysis is a potential alternative for routine clinical screening of the common types of alpha- and beta-thalassemia large gene deletions, since it is simple, cost-effective, and highly accurate.