China
Africa
Explore chapters and articles related to this topic
HLA-DR and -DQ Typing by DNA-RFLP Analysis
Published in M. Kam, Jeffrey L. Bidwell, Handbook of HLA TYPING TECHNIQUES, 2020
DNA-restriction fragment length polymorphism (RFLP) typing is a well-established technique for routine identification of HLA-DR and -DQ allotypes. Methods and an interpretation scheme are presented which permit the identification of HLA-DR and -DQ allotypes using a single restriction endonuclease, TaqI. Resolution between problematic specificities may be rapidly achieved by simple polymerase chain reaction (PCR) -based supplementary tests.
Argininemia
Published in William L. Nyhan, Georg F. Hoffmann, Aida I. Al-Aqeel, Bruce A. Barshop, Atlas of Inherited Metabolic Diseases, 2020
William L. Nyhan, Georg F. Hoffmann, Aida I. Al-Aqeel, Bruce A. Barshop
The human gene at chromosome 6q23.2 is 11.5 kb in size and contains 18 exons [32]. The crystal structure of the enzyme has been elucidated [31, 33]. A dimagnesium cluster is essential for enzymatic activity and stability of the protein [34]. Mutation analysis revealed no gross deletions by Southern blot analysis in 15 patients [9]. In three, a TaqI restriction enzyme cleavage site was missing. In two of these, mutations were identified. One was homozygous for R291Y (an arginine-to-tyrosine change) and the other heterozygous for T290S (a threonine-to-serine change). A Japanese patient was found to be a compound in which, on one allele, there was a four-base deletion in exon 3, which caused a frameshift at position 87 and a premature termination 45 residues later while, on the other allele, a single base deletion in exon 2 led to a frameshift at 26 and premature termination on five residues later [10]. In another study of Japanese patients [35], the mutations found were in W122X, 6235R, and L282 frameshift. The enzyme activities assayed in expression studies in E. coli were zero, consistent with enzyme assays in the erythrocytes of patients. Mutations in ARG1 though heterogeneous have largely been point mutations and microdeletions rather than major or structural alternations in the gene, indicating extensive genetic heterogeneity [8, 11].
Liver Cancer
Published in Peter G. Shields, Cancer Risk Assessment, 2005
Christopher Loffredo, Christina Frank
Genetic variations among individuals in their capacity to detoxify ethanol may play an additional role in susceptibility to HCC. Ethanol metabolism is mediated by several enzymes, including alcohol dehydrogenase and cytochrome p450 2E1, both of which are encoded by genes known to be polymorphic in populations. Individuals with mutations in one or both of these genes may be at greater or lesser risk from ethanol toxicity depending on the phenotypic consequences of the mutations. A meta-analysis of the RsaI polymorphism in the CYP2E1 gene revealed no association with alcoholic liver disease nor with HCC, while the TaqI allele was significantly less prevalent in persons with alcoholic liver disease compared to healthy subjects (129), suggesting a protective effect. However, there is no direct evidence that the TaqI allele alters the metabolism of ethanol, and the apparent protective effect might be due to linkage disequilibrium with other, unidentified protective genes or factors. More research is clearly needed on this topic.
Vitamin D Receptor (VDR) Allelic Variants Correlating with Response to Vitamin D3 Supplementation in Breast Cancer Survivors
Published in Nutrition and Cancer, 2022
Elham Kazemian, Sayed Hossein Davoodi, Mohammad Esmaeil Akbari, Nariman Moradi, Safoora Gharibzadeh, Alison M Mondul, Yasaman Jamshidi-Naeini, Maryam Khademolmele, Katie R. Zarins, Nasim Ghodoosi, Laura S. Rozek, Atieh Amouzegar
It is hypothesized that VDR expression and function including receptor affinity, binding to nuclear DNA and RNA transcription may be influenced by variation in the VDR gene (28). The 3′ BsmI, ApaI, and TaqI allelic sequence variants are considered to be silent SNPs which do not alter the amino acid sequence of the translated protein (28). However, they are in LD with one or more functional SNPs elsewhere in the VDR gene (28). In addition, the sequence variants identified near the 3′ region of VDR, including BsmI, ApaI and Taq1, contributed to the regulation of mRNA stability, half-life and translational activity (29,67,68). Additionally, FokI SNP results in generation of altered VDR protein activity while Cdx2 could alter the transcription activity of the VDR promoter region (29,30).
Association of VDR gene polymorphisms with risk of relapsing-remitting multiple sclerosis in an Iranian Kurdish population
Published in International Journal of Neuroscience, 2018
Rasoul Abdollahzadeh, Parisa Moradi Pordanjani, Farideh Rahmani, Fatemeh Mashayekhi, Asaad Azarnezhad, Yaser Mansoori
TaqI was the second studied polymorphism in which significant differences in genotype and allele frequencies (except heterozygous TC) were observed between cases and controls. Allele C showed a positive association with MS and its frequency was higher in patients (46.2%) than controls (30.2%). As it was expected, TT genotype showed a negative correlation with the disease, while the CC genotype revealed to be positively associated with MS. Although no significant difference was observed between patients and controls for TC genotype, it was close to significant value. Considering a dominant genetic model, combined TT + TC vs. CC found to be significantly different between two groups with a protective role against the disease; however, combined CC + TC compared to TT genotype was a susceptibility recessive genetic model associated with risk of MS. There are several studies consistent with our findings [13,19,26,27,31], nonetheless, a few other reports are in contrast with ours [18,24,25,32,33]. These findings explain that allele T and TT genotype seem to be directly or indirectly by LD with other variants introduce susceptibility risk to MS; however, carriers of allele C and CC genotype might be more protected against the disease.
Vitamin D receptor gene polymorphisms and risk of polycystic ovary syndrome in South Indian women
Published in Gynecological Endocrinology, 2018
Swapna Siddamalla, Tumu Venkat Reddy, Suresh Govatati, Nagendram Erram, Mamata Deenadayal, Sisinthy Shivaji, Manjula Bhanoori
VDR BsmI, ApaI and TaqI polymorphisms were analyzed by means of polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) method as described earlier [20]. The primers and PCR conditions used were given in Table 1. PCRs were carried out in a total volume of 25 μl, containing 50 ng genomic DNA, 2–6 pmole of each primer, 1× Taq polymerase buffer (1.5 mM MgCl2) and 0.5 U of Amplitaq DNA polymerase (Perkin Elmer, Foster City, CA). The PCR products were digested with restriction enzymes (BsmI at 65 °C, ApaI at 25 °C, and TaqI at 65 °C) for 3 h and the DNA fragments were electrophoresed through a 2% agarose gel and stained with ethidium bromide. For the VDR BsmI A/G SNP, the A allele was represented by DNA band of size 514 bp, the G allele was represented by DNA bands of sizes 338 and 176 bp; whereas, the heterozygotes displayed a combination of both alleles (514, 338 and 176 bp). ApaI A/C SNP, the A allele was represented by DNA band of size 352 bp and the C allele was by a DNA band of size 213 and 139 bp, and heterozygotes displayed a combination of both alleles (352, 213 and 139 bp) . TaqI T/C SNP, the T allele was represented by DNA band of size 352 bp, the C allele was represented by DNA bands of sizes 293 and 59 bp; whereas, the heterozygotes displayed a combination of both alleles (352, 293 and 59 bp) (Figure 1). The results were confirmed by PCR–DNA sequencing with a Taq-Dye deoxy-terminator cycle sequencing kit (Applied BioSystems, Foster City, CA) using an automated ABI 3770 DNA sequencer (Applied BioSystems). Genotype calling was performed using Chromas V0.2 software (Technelysium Pty Ltd, South Brisbane, Australia).