Cytochrome P450 (CYP2C9*2,*3) & vitamin-K epoxide reductase complex (VKORC1 -1639G<A) gene polymorphisms & their effect on acenocoumarol dose in patients with mechanical heart valve replacement.

Background & objectives: Studies have demonstrated the effect of CYP2C9 (cytochrome P450) and VKORC1 (vitamin K epoxide reductase complex) gene polymorphisms on the dose of acenocoumarol. The data from India about these gene polymorphisms and their effects on acenocoumarol dose are scarce. The aim of this study was to determine the occurrence of CYP2C9*2,*3 and VKORC 1 -1639G>A gene polymorphisms and to study their effects on the dose of acenocoumarol required to maintain a target International Normalized Ratio (INR) in patients with mechanical heart valve replacement. Methods: Patients from the anticoagulation clinic of a tertiary care hospital in north India were studied. The anticoagulation profile, INR (International Normalized Ratio) values and administered acenocoumarol dose were obtained from the clinical records of patients. Determination of the CYP2C9*2,*3 and VKORC1 -1639G>A genotypes was done by PCR-RFLP (restriction fragment length polymorphism). Results: A total of 111 patients were studied. The genotype frequencies of CYP2C9 *1/*1,*1/*2,*1/*3 were as 0.883, 0.072, 0.036 and that of VKORC1 -1639G>A for GG, AG, and AA genotypes were 0.883, 0.090, and 0.027, respectively. The percentage of patients carrying any of the variant alleles of CYP2C9 and VKORC1 in heterozygous or homozygous form was 34% among those receiving a low dose of ≤20 mg/wk while it was 13.8 per cent in those receiving >20 mg/wk (P=0.014). A tendency of lower dose requirements was seen among carriers of the studied polymorphisms. There was considerable variability in the dose requirements of patients with and without variant alleles. Interpretation & conclusions: The study findings point towards the role of CYP2C9 and VKORC1 gene polymorphisms in determining the inter-individual dose variability of acenocoumarol in the Indian patients with mechanical heart valve replacement.

Does cytokine gene polymorphism affect steroid responses in idiopathic nephrotic syndrome?

Background: Immunological responses may be possibly involved in the pathogenesis of idiopathic nephrotic syndrome (INS). Cytokines act as a potent immunomodulator. Pathogenesis of INS is associated with Th1 and Th2 cytokines imbalance. Aims, Settings and Design: We have investigated the association of IL-4, IL-6, and TNF-alpha gene polymorphisms and analyzed the data to evaluate the effect of these polymorphisms on the pathogenesis and clinical course of INS. Materials and Methods: One hundred fifty children with INS were selected. Children were analyzed for IL-4, IL-6, and TNF-alpha gene polymorphisms by using polymerase chain reaction and restriction fragment length polymorphism. Statistical Analysis Used: Chi-square test was used for different comparisons. The synergistic effects of IL-4, IL-6, and TNF-alpha gene polymorphisms were evaluated by using logistic regression analysis. Results and Conclusions: We compared the steroid-resistant (SR) and steroid-responsive (SS) groups. Our results showed strong association of IL-6 -G174C, and IL-4 -C590T at genotypic level (P = 0.0121, OR = 14.71, 95% CI = 1.59-136.46; and P = 0.0386, OR = 7.29, 95% CI = 1.26-41.69). TNF-alpha revealed a strong association at genotypic level (P = 0.0121, OR = 14.71, 95% CI = 1.59-136.46), as well as at allelic level (P = 0.0433, OR = 2.251, 95% CI = 1.09-4.66), demonstrating that it may be considered one of the genetic risk factors affecting the steroid response in INS patients. The GG genotype of IL-6 -G174C, TT genotype of IL-4 -C590T, and AA genotype of TNF-alpha -G308A cytokine gene polymorphisms may be causative factors for nonresponsiveness towards steroid therapy among INS children.

Human genetic variation and personalized medicine.

Human genome sequencing results revealed an insight into the role of human genetic variation behind differential susceptibility of human diseases, differential response to pharmacological agents and presence of varied phenotypes. This leads to the concept of personalized medicine. In the present review we have discussed the objectives and approaches for carrying out pharmacogenomics and pharmacogenetics studies. The review also incorporates the major findings categorizing the common diseases on the basis of genetic profiles and ethnic information and in establishing personalized disease diagnosis, drug responses and treatment modalities based on the genetic determinants. Overall an attempt has been made to highlight the importance of studying the genetic profiles of an individual in biomedical and pharmacogenomics research.

S252W mutation in Indian patients of Apert syndrome.

Two common mutations in the exon IIIa of fibroblast growth factor receptor 2 account for majority of the cases of Apert syndrome. They can be analyzed by amplifying the segment followed by testing for the abolition of restriction sites. We evaluated two children with typical features of Apert syndrome. A segment of FGFR2 exon IIIa was amplified by polymerase chain reaction. Restriction fragment length polymorphism was analyzed using enzymes MboI and BglI respectively for S252W and P253R mutations. The DNA segment was sequenced using ABI 310 automated DNA fragment analyzer. Both the patients showed S252W mutations. DNA sequencing confirmed the results of the restriction fragment length polymorphism. Our study is the first report from Indian subcontinent to show the prevalence of S252W mutation among Apert syndrome patients from Indian origin.

TNFR2 gene polymorphism in coronary artery disease.

BACKGROUND: Recently atherosclerosis and coronary artery disease (CAD) are considered to be inflammatory diseases. The genetic polymorphism in inflammatory markers has been well studied and found to be associated with development of CAD. AIM: To study the association of biallelic polymorphism at position 196 in exon 6 of tumor necrosis factor 2 (TNFR2) gene and coronary artery disease. SETTINGS AND DESIGN: The study design was a prospective case control study conducted at a tertiary referral center mainly catering to the north Indian population. MATERIALS AND METHODS: One hundred and fifty angiographically proven patients with coronary artery disease and one hundred and fifty age matched controls were genotyped for TNFR2 gene by polymerase chain reaction followed by analysis of restriction fragment length polymorphism. STATISTICAL ANALYSIS: Genotype frequencies were compared in patients and controls by Chi-square test. Binary logistic regression analysis was used to examine the relationship between genotypes and disease, incorporating other variables into the model. RESULTS: The incidence of CAD in those with MM genotype was 65% and in those with RM genotype was 42%. Genotype frequency shows significant association of MM genotype with development of CAD (P < 0.001; odds ratio-2.585; 95% confidence interval 1.533-4.359). The association of TNFR2 genotype with CAD persisted on logistic regression analysis. CONCLUSION: MM genotype of TNFR2 gene is associated with development of CAD and RM genotype appears to be protective.

Short tandem repeat technology has diverse applications: individual identification, phylogenetic reconstruction and chimerism based post haematopoietic stem cell transplantation graft monitoring.

BACKGROUND: Short Tandem Repeat (STR) loci are widely considered to be effective for variety of applications including forensic applications, phylogenetic reconstruction and chimerism based post Haematopoietic Stem Cell Transplantation (HSCT) graft monitoring. For each application, specific sets of STR loci are used. AIMS: In the present study, we have attempted to use same set of STR loci for varied purposes based on their efficacy and informativity. SETTINGS AND DESIGN: Population and patient based study. MATERIALS AND METHODS: We have analyzed 5 STR loci--vWA, Tho1, FES, F13 and TPOX in 1000 North Indians. All five markers were also analyzed for chimerism based graft monitoring after HSCT in 42 HLA matched pair of patient-donor to predict the outcome of transplantation. STATISTICAL ANALYSIS: The analysis was done for Hardy Weinberg equilibrium (HWE), Heterozygosity, Polymorphism information content (PIC) and Power of Exclusion and Phylogenetic assessment. RESULTS AND CONCLUSIONS: High allelic variability in term of Heterozygosity (0.68-0.76), PIC (0.66-0.74) and high Power of exclusion (0.28-0.38) indicating high forensic utility. The ensuing PC plots finely resolved three basal clusters corresponding to three geo-ethnic groups of African, Orientals, and Caucasians. In post HSCT chimerism analysis, it was found that together these markers were informative in 38 pairs (98%) and were able to predict the chimerism status successfully. There is a possibility that these STR loci along with forensic and phylogenetic importance, can predict the outcome of HSCT successfully.

Angiotensin-converting enzyme gene polymorphism in coronary artery disease in north India.

BACKGROUND: The aim of this study was to investigate the role of angiotensin-converting enzyme gene polymorphism in patients with coronary artery disease in north India. METHODS AND RESULTS: One hundred forty-six patients with angiographically proven atherosclerotic coronary artery disease, and 146 age- and sex-matched control subjects (treadmill-negative) were included in the study. Genomic DNA was extracted and analyzed for angiotensin-converting enzyme insertion/deletion polymorphism. Two independent investigators scored the genotypes. CONCLUSIONS: When we compared the genotypes of patients with coronary artery disease with those of normal controls, it was seen that all three genotypes, i.e. DD, ID and II, were not statistically different among patients and controls. Further, we categorized the patient and control groups into 2 subgroups, i.e. below and above 50 years of age. Interestingly, it was observed that the DD genotype was significantly higher in patients in the higher age group (i.e. above 50 years of age). However, this needs further validation by studying patients with coronary artery disease from other parts of India.

Seroanalysis of Chlamydia trachomatis and S-TORCH agents in women with recurrent spontaneous abortions.

Genital tract infections are an important cause of pregnancy loss, many of which are amenable to treatment. There is scarcity of literature on role of S-TORCH agents in recurrent spontaneous abortions (RSA) and available data on role of Chlamydia trachomatis (CT) is controversial. In a retrospective analysis, CT IgM, IgG and IgA antibodies were tested by indirect ELISA in 86, 53 and 30 sera samples respectively from women with RSA (= or > 3 abortions). IgM antibodies using m-capture ELISA for S-TORCH agents (Syphilis, tested by VDRL) were analysed in 47 sera from women with RSA. Results compared with 29 age matched normal pregnant women. Anatomical, endocrine, Rh incompatibility and chromosomal abnormality in the couple were ruled out prior to inclusion in the study. Serum anti-CT IgM positivity was 46.5% in RSA vs. 13.8% in control group (p < 0.001). S-TORCH positivity in RSA group was 31.9% and nil in the control group (p < 0.005). Present study demonstrates a strong association between IgM antibodies to CT and S-TORCH agents in women with history of RSA.

Polymorphisms in the apolipoprotein B-100 gene: association with plasma lipid concentration and coronary artery disease.

BACKGROUND: The aim of this study was to investigate the association of apolipoprotein B gene polymorphisms with coronary artery disease and lipid levels in Indians. METHODS AND RESULTS: One hundred patients of angiographically proven atherosclerotic coronary artery disease and one hundred age- and sex-matched control subjects (treadmill negative) were included in the study. Serum lipids including cholesterol, triglycerides, high-density lipoprotein, low-density lipoprotein, very low-density lipoprotein, and apolipoprotein B were analyzed. Genomic DNA was extracted and the apolipoprotein B 3' hypervariable region amplified by polymerase chain reaction. Regions carrying Xba1, EcoR1, and Msp1 restriction sites present in the apolipoprotein B gene were amplified and digested separately by the respective enzymes. Restriction fragment length polymorphism analysis showed that EcoR1 with the R+/R+ genotype was significantly more common in patients with coronary artery disease. Overall, the genotypes EcoR1+/+, Msp1+/+, Xba1+/+ and Eco R1+/+ Msp1+/-, Xba1-/- were significantly more common in patients as compared to controls (p<0.05). When gene polymorphisms were compared with lipid abnormalities, the genotypes EcoR1+/+, Xba1-/-, and Msp1+/+ were more frequent in patients with elevated apolipoprotein B and very low-density lipoprotein levels. On the other hand, these genotypes were less common in patients with increased total cholesterol and low-density lipoprotein levels. When we studied the individual alleles of the variable number of tandem repeats region, we observed that allele 34 was significantly increased in patients with coronary artery disease as compared to controls. Allele 36 was present with a frequency of 1% in controls while it was totally absent in patients. CONCLUSIONS: This study identifies the apolipoprotein B gene polymorphism associated with coronary artery disease. An association between apolipoprotein B gene polymorphisms and elevated apolipoprotein B and very low-density lipoprotein levels was observed. However, there was no positive association with other elevated lipid levels in North Indians from Uttar Pradesh.

HLA and bone marrow transplant donor search strategies.

Searching for a family donor other than an HLA identical sibling can be successful. The chance of finding an identical or one antigen mismatched family donor can be calculated with a computer program, so this may help in the decision making whether to perform extended family typing or not. Extended family donors are often better matched rather than unrelated donors. The reason is that they have at least one haplotype genetically identical to the patient, and that there may be some higher match grade for the minor histocompatibility antigens. Sometimes extended family donor could be the only donor for the patient. Ethical considerations have to be taken into account and extended family donors should be volunteer donors.

HLA Antigen And Haplotype Frequencies In Bhargavas And Chaturvedies Of UP (India).

In the present study, two endogamous caste groups of U.P., viz; Bhargavas and Chaturvedies, subgroups of the major ethnic group of Brahmins were typed for HLA antigen and haplotype frequencies. Gene pools of these two groups may be unique and well preserved because of socio-cultural barriers and strict endogamy. Our results revealed that these two populations are indeed different from each other and that the different populations of India cannot be considered as a single panmictic population.