Whole-genome sequencing of clinical isolates from tuberculosis patients in India: real-world data indicates a high proportion of pre-XDR cases.

Treatment decisions for tuberculosis (TB) in the absence of full drug-susceptibility data can result in amplifying resistance and may compromise treatment outcomes. Genomics of Mycobacterium tuberculosis (M.tb) from clinical samples enables detection of drug resistance to multiple drugs. We performed whole-genome sequencing (WGS) for 600 clinical samples from patients with tuberculosis to identify the drug-resistance profile and mutation spectrum. We documented the reasons reported by clinicians for referral. WGS identified a high proportion (51%) of pre-extensively drug-resistant (pre-XDR) cases followed by multidrug-resistant tuberculosis (MDR-TB) (15.5%). This correlates with the primary reason for referral, as non-response to the first-line treatment (67%) and treatment failure or rifampicin resistance (14%). Multivariate analysis indicated that all young age groups (P < 0.05), male gender (P < 0.05), and Beijing strain (P < 0.01) were significant independent predictors of MDR-TB or MDR-TB+ [pre-extensively drug-resistant tuberculosis (XDR-TB) and XDR-TB]. Ser315Thr (72.5%) in the inhA gene and Ser450Leu in the rpoB gene (65.5%) were the most prevalent mutations, as were resistance-conferring mutations to pyrazinamide (41%) and streptomycin (61.33%). Mutations outside the rifampicin resistance-determining region (RRDR), Ile491Phe and Val170Phe, were seen in 1.3% of cases; disputed mutations in rpoB (Asp435Tyr, His445Asn, His445Leu, and Leu430Pro) were seen in 6% of cases, and mutations to newer drugs such as bedaquiline and linezolid in 1.0% and 7.5% of cases, respectively. This study on clinical samples highlights that there is a high proportion of pre-XDR cases and emerging resistance to newer drugs; ongoing transmission of these strains can cause serious threat to public health; and whole-genome sequencing can effectively identify and support precision medicine for TB. IMPORTANCE: The current study is based on real-world data on the TB drug-resistance profile by whole-genome sequencing of 600 clinical samples from patients with TB in India. This study indicates the clinicians' reasons for sending samples for WGS, which is for difficult-to-treat cases and/or relapse and treatment failure. The study reports a significant proportion of cases with pre-XDR-TB strains that warrant policy makers' attention. It reflects the current iterative nature of the diagnostic tests under programmatic conditions that leads to delays in appropriate diagnosis and empirical treatment. India had an estimated burden of 2.95 million TB cases in 2020 and 135,000 multidrug-resistant cases. However, WGS profiles of M.tb from India remains disproportionately poorly represented. This study adds a significant body of data on the mutation profiles seen in M.tb isolated from patients with TB in India, mutations outside the RRDR, disputed mutations, and resistance-conferring mutations to newer drugs such as bedaquiline and linezolid.

Spinocerebellar Ataxias in India: Three­year Molecular Data from a Central Reference Laboratory.

INTRODUCTION: There is a great deal of heterogeneity, both phenotypically and genotypically among the autosomal dominant cerebellar ataxias (ADCA). Their prevalence also varies in different populations. Trinucleotide repeat expansions (CTG/CAG) have been shown predominantly to cause a number of ADCAs. AIM: The present study describes the frequency of spinocerebellar ataxias (SCA) and the CAG repeat sizes among the different regions of India. SETTINGS AND DESIGN: Molecular data from our central reference laboratory were retrospectively analyzed for SCAs 1, 2, 3, 6, 7, 10, 12, 17 and DRPLA. Correlation between age at diagnosis and the CAG repeats of the expanded and the normal alleles were tested with the Spearman correlation test. RESULTS: The presence of SCAs vary according to geographical regions and ethnicities; SCA 12 was detected with the highest frequency (229/901), but was restricted to a specific ethnic population, followed by SCA 2 with a positivity of 12% (101/845). SCA 3 previously known as Machado-Joseph Disease had a prevalence of 4.05% (32/789), whereas SCA 1 was diagnosed in 30/773 (3.88%). No positivity was seen for SCA 10 from the 103 samples tested and for SCA 17 from the 131 samples tested either as a part of an extended panel or stand-alone. CONCLUSION: In this report, we are able to expand the portrait of SCAs in India by presenting the largest ever molecular data from a central reference laboratory.

The contribution of childhood adversity to cortisol measures of early life stress amongst infants in rural India: Findings from the early life stress sub-study of the SPRING cluster randomised controlled trial (SPRING-ELS).

BACKGROUND: The majority of the world's children live in low- and middle-income countries and face multiple obstacles to optimal wellbeing. The mechanisms by which adversities - social, cultural, psychological, environmental, economic - get 'under the skin' in the early days of life and become biologically embedded remain an important line of enquiry. We therefore examined the contribution of childhood adversity through pregnancy and the first year of life to hair and salivary cortisol measures of early life stress in the India SPRING home visits cluster RCT which aims to improve early childhood development. METHODS: We assessed 22 adversities across four domains: socioeconomic, maternal stress, family-child relationship, and child and summed them to make a cumulative adversity score & quintiles, and four subscale scores. We cut 3 cm of hair from the posterior vertex and took three saliva samples from morning till late afternoon on each of two days (total six samples). We analysed both for cortisol concentration using ELISA techniques. We used multiple linear regression techniques to assess the relationship between cumulative adversity and log hair cortisol concentration and saliva diurnal slope and area under the curve. RESULTS: We assessed 712 children for hair, and 752 children for saliva cortisol at 12 months of age. We found a strong positive relationship between adversity and hair cortisol; each additional adversity factor was associated with hair cortisol increases of 6.1% (95% CI 2.8, 9.4, p < 0.001) and the increase from adversity quintile one to five was 59.4%. Socioeconomic, relationship and child scales were independent predictors of hair cortisol (socioeconomic 6.4% (95% CI -0.4, 13.6); relationship 11.8% (95% CI 1.4, 23.2); child 7.9% (95% CI -0.5, 16.9). We did not find any association between any measures of adversity and either of the saliva cortisol outcomes. DISCUSSION: This is the largest study of hair cortisol in young children, and the first in a low- and middle-income country setting. Whilst the short-term diurnal measures of cortisol did not appear to be linked with adversity, chronic exposure over several months appears to be strongly associated with cumulative adversity. These findings should spur further work to understand the specific ways in which adversity becomes biologically embedded, and how this can be tackled. They also lend support to ongoing action to tackle childhood adversity in communities around the world.

Status of TMPRSS2-ERG fusion in prostate cancer patients from India: correlation with clinico-pathological details and TMPRSS2 Met160Val polymorphism.

BACKGROUND: Prostate cancer (PCa) shows considerable clinical heterogeneity that has been primarily attributed to variable molecular alterations. TMPRSS2-ERG fusion is one such molecular subtype that has been associated with predominantly poor prognosis. More recently, a single nucleotide polymorphism (SNP) in the TMPRSS2 gene rs12329760 C>T (Met160Val) has been shown to positively correlate with the fusion status and also to be associated with increased risk for PCa. The aim of the present study is to determine the frequency of TMPRSS2-ERG fusion and association of rs12329760 in Indian PCa patients with fusion status. METHODS: TMPRSS2-ERG fusion by fluorescence in situ hybridization was determined in 102 of 150 PCa biopsy-proven cases. Genotyping for rs12329760 was performed on the entire cohort of 150 cases by Sanger sequencing. RESULTS: TMPRSS2-ERG fusion was seen in 27 of 102 (26%) cases. Fusion-positive patterns in this study showed fusion by translocation in nine of 27 cases (33.5%), by deletion in six of 27 (22%) cases, and by insertion in 12 of 27 cases (44.5%). No association of the fusion status with Gleason Score, pattern, or perineural invasion was seen. The TMPRSS2 SNP rs12329760 'T' allele was prevalent with a frequency of 0.27 in the PCa patients. The SNP was significantly associated with fusion [odds ratio (OR) = 2.176, 95% confidence interval (CI) = 1.012-4.684, P = 0.04], more specifically fusion by deletion (P = 0.04). CONCLUSION: The results provided here determine the frequency of TMPRSS2-ERG fusions (26%) in a fairly large cohort of Indian PCa cases and also the association of rs12329760 SNP with TMPRSS2-ERG fusion. No association with other clinico-pathological features was observed. Future studies with clinical outcomes are warranted in this population.

Frequency and association of disabled homolog 2-interacting protein (DAB2IP) variant rs7025486 G>A with coronary artery disease risk in Indian population.

Genome wide association study has identified rs7025486 G>A polymorphism within DAB2IP (Disabled homolog 2-interacting protein) gene with increased risk of coronary heart disease (CAD). In this study we have determined the frequency and association of rs7025486 with CAD in Indians. The study was performed on 214 patients with CAD and 125 controls. The 'AA' genotype was associated with an increased risk in the CAD age group <50 yrs as compared to CAD age group>50 yrs (OR 3.149; P 0.034) and controls >50 yrs (OR 3.430; P 0.080). The risk allele (A) was significantly associated with premature CAD.

Association of Genetic Variants at the 4q25 Locus with Atrial Fibrillation in Indian Population.

INTRODUCTION: Atrial fibrillation (AF) is the most common cardiac arrhythmia in clinical settings known to impair cardiac function. Genome-wide association studies identified SNPs on chromosome 4q25 to be associated with AF. Till date no information is available from India related to the association of these variants with AF. MATERIALS AND METHODS: Two hundred and sixty-seven individuals comprising of 170 patients with Coronary Artery Disease (CAD), 41 patients with AF, and 56 healthy controls were genotyped for rs10033464 and rs2200733 at 4q25 locus. RESULTS: Strong association of rs10033464 with AF was observed on comparison with control groups (OR: 2.59; 95% CI: 1.08-6.21; P: 0.031) and between post-coronary artery bypass grafting (CABG) AF and control with dominant genetic model (OR: 4.73; 95% CI: 1.50-14.89; P: 0.0071). Comparison of post-CABG AF with CAD also indicated association (OR: 2.73; 95% CI: 0.9-7.56; P value: 0.05). In contrast, the rs2200733 C>T variant did not show any association with post-CABG AF, but with lone AF with the 'T' allele being associated with increased risk was seen (OR: 2.80; 95% CI: 1.08-7.24; P value: 0.042). CONCLUSION: In conclusion, the rs10033464 (T) allele is associated with the risk of post-CABG AF and the rs2200733 (T) with lone AF.

Hb F Levels in Indian Sickle Cell Patients and Association with the HBB Locus Variant rs10128556 (C>T), and the HBG XmnI (Arab-Indian) Variant.

The prevalence of sickle cell disease in India is very high. Hb F is one of the most powerful modulators of disease severity in sickle cell disease patients. It was traditionally thought that the disease is milder in Indian sickle cell disease patients predominantly due to the Arab-Indian haplotype characterized by the HBG XmnI [rs7482144 (G>A)] variant, which is associated with increased Hb F levels. In the current study, we investigated the Hb F levels in individuals with the rs10128556 (C>T) variant and also determined its linkage with the HBG XmnI variant. The present study was conducted on a cohort of 275 individuals, which consisted of 221 patients with sickle cell disease and 54 patients with sickle cell trait. Analysis of hemoglobin (Hb) fractions and variants was done on the high performance liquid chromatography (HPLC) system. Genotyping for rs10128556 was done by direct sequencing of the products. Mean Hb F levels in the sickle cell disease patients was 19.36 ± 6.79. The genotypic frequencies for rs10128556 were 82.0% (TT), 16.7% (CT) and 1.3% (CC) for sickle cell disease patients. The minor C allele resulted in 52.0% decrease in Hb F levels when homozygous and 7.0% decrease when heterozygous. The rs10128556 single nucleotide polymorphism (SNP) was in strong but not complete linkage with the HBG XmnI variant. In conclusion, the study determined for the first time the frequency and association of rs10128556 in Indian sickle cell disease patients with Hb F. It also established that it was not in complete linkage with the HBG XmnI variant in this high risk population.

Homozygous c.1160C>T (P38L) in the MECP2 gene in a female Rett syndrome patient.

Rett syndrome is a severe X-linked dominant neurodevelopmental disorder. Mutations in the MECP2 gene on chromosome Xq28 have been shown to be the cause of Rett syndrome. Sequencing of the MECP2 gene in a patient with clinical suspicion of Rett syndrome revealed c.1160C>T (P387L) in exon 4 of the MECP2 gene homozygously. Females with Rett syndrome are usually heterozygous for a mutation in MECP2. Uniparental disomy as a probable cause for the homozygous presence of this mutation was ruled out by quantitative fluorescence-polymerase chain reaction. Moreover to our knowledge this mutation has only been reported in males with X-linked mental retardation (MRX). We hypothesize that the presence of this mutation c.1160C>T (P387L) in the homozygous form is responsible for the Rett syndrome-like phenotype seen in this patient. This novel report reveals for the first time the homozygous presence of a mutation which has hitherto only been reported in males with MRX.

Genetics of fetal hemoglobin in tribal Indian patients with sickle cell anemia.

India tops the list of countries with sickle cell disease (SCD) with an estimated 44,000 live births in 2010 and a prevalence of 10%-33%. In the present study, the first from India, we have investigated the effect of genetic variants in the BCL11A, the HMIP (HBS1L-MYB intergenic polymorphism) locus, in addition to the HBB locus, which are known to be associated with fetal hemoglobin (HbF) levels, a major modulator of the disease phenotype. The present study was conducted on 240 individuals with SCD and 60 with sickle cell trait. Genotyping was performed for the BCL11A rs11886868 and rs34211119; HMIP rs9399137, rs189600565, rs7776196, rs34778774, and rs53293029; HBG2 Xmn1 polymorphism rs7482144; and -68C > T HBD promoter polymorphism. All the 3 quantitative trait loci were associated with HbF levels in Indian patients with SCD. The highest difference was seen in the Xmn1 single-nucleotide polymorphism, which accounted for 11% of the trait variance, the BCL11A rs11886868 for 3.65%, whereas the HMIP rs9399137 for 3.8%. The present study indicates the BCL11A, HMIP, and ß-globin region to be associated with increased HbF levels in Indian patient. Further interrogation of these genotypes with respect to pain crisis is warranted in this population, which may help in prognostication, as also a genome-wide association study, which may help uncover new loci controlling HbF levels.

Genetic variant in the BCL11A (rs1427407), but not HBS1-MYB (rs6934903) loci associate with fetal hemoglobin levels in Indian sickle cell disease patients.

India along with Nigeria and DRC contribute to 57% of the world sickle cell anemia population. The annual number of newborns in India with SCA was estimated at 44,000 in 2010. Even with this high prevalence there is minimal information about genetic factors that influence the disease course in Indian patients. The current study was conducted on 240 patients with SCD and 60 with sickle cell trait, to determine the association of genetic variants at the BCL11A (rs1427407) and HBS1-MYB (rs6934903) loci with fetal hemoglobin levels (HbF). Both these loci have been implicated with influencing HbF levels, a powerful modulator of the clinical and hematologic features of SCD. Our results indicate the BCL11A rs1427407 G>T variant to be significantly associated with HbF levels {19.12±6.61 (GG), 20.27±6.92 (GT) and 24.83±2.92 (TT) respectively} contributing to ~23% of the trait variance. Interestingly no association of the HBS1L-MYB rs6934903 with the HbF levels was seen. The present study indicates the BCL11A (rs1427407) but not HMIP (rs6934903) to be associated with elevated HbF levels in Indian patient. Further interrogation of additional variants at both the loci; as also a GWAS which may help uncover new loci controlling HbF levels.

Pedometer assessed physical activity in urban pubertal children: first report from India.

BACKGROUND: Inadequate physical activity is a risk factor for several lifestyle diseases. In the current study we have tried to evaluate the physical activity levels in urban Indian pubertal children as well as investigate the relationship between step counts and body composition. METHODS: A total of 1032 children aged 12 to 15 years wore pedometers for 2 weekdays and 2 weekend days, the final cohort included 910 subjects with 467 boys and 443 girls. RESULTS: Mean weekday steps were 11,062 ± 4741 for boys and 9619 ± 4144 for girls; weekend steps were 10,842 ± 5034 for boys and 9146 ± 5159 for girls, which were both significantly different. The weekend steps were consistently lower in both genders. Analysis of children not meeting a cut-off of 10,000 steps indicated that 45% of the boys aged 12; 54% aged 13; 43% to 48% aged 14 and 50% in the aged 15 did not meet the cut-off. In girls higher levels of inactivity were seen with 58% to 65% aged 12; 69% to 73% aged 13; 49% to 58% aged 14 and 50% to 100% in age-group 15 did not meet the cut-off on weekdays and weekends respectively. CONCLUSIONS: The high level of physical inactivity in the representative urban Indian children is a cause of grave concern and necessitates urgent intervention strategies to be formulated.

Variant at 9p21 rs1333049 is associated with age of onset of coronary artery disease in a Western Indian population: a case control association study.

The 9p21 chromosomal region has been associated with coronary artery disease (CAD) in many genome wide association studies (GWAS). To date no information exists regarding the rs1333039 SNP which showed the strongest association in the WTCCC GWAS with CAD risk in the Indian population. The present study attempts to replicate the findings in the Indian population. Genotyping for rs1333049 was done in 229 cases and 151 controls by allele-specific real-time assay. A higher frequency of the risk allele rs1333049C was seen in cases (0·60) as compared with controls (0·49), which associated with CAD risk both in univariate (OR = 1·564, 95%CI = 1·154-2·119, P = 0·003) and multivariate analysis (OR = 2·460, 95%CI = 1·139-5·314, P = 0·022). Increased frequency of the risk allele was seen in younger individuals with CAD where 40% individuals in the age group 30-55 years had the CC genotype as compared with 29 and 24·5% in the age group 56-65 years and > 65 years, respectively (CC versus GG, P = 0·045). Higher incidence of the CC genotype was seen in MI patients, but missed significance when compared with controls (OR = 1·361, 95%CI = 0·954-1·942, P = 0·084). In conclusion, the rs1333049 variant is significantly associated with CAD risk and also with age of onset in the Western Indian population. However there are differences in the haplotype structure of this SNP with the neighbouring rs10757278 SNP, these differences emphasize the importance of genotyping all risk variants at this locus which could underlie the differences in risk susceptibility to CAD across populations.

Promoter variants in interleukin-6 and tumor necrosis factor alpha and risk of coronary artery disease in a population from Western India.

INTRODUCTION: A central component of the atherosclerotic process is inflammation. Single nucleotide polymorphisms (SNPs) present in the promoter region of various cytokines can lead to altered levels of the transcript and a state of low-grade inflammation exacerbating the risk of coronary artery disease (CAD). The present work tries to understand the role of permissive promoter variants in the interleukin-6 gene (IL-6-174G/C) and the tumor necrosis factor alpha (TNFα-308G/A) in the causation of CAD and also dyslipidemia. MATERIALS AND METHODS: Genotyping was conducted on 100 cases of CAD and 150 controls by the allele termination assay SNaPshot. Biochemical parameters were determined by routine enzymatic endpoint methods. The results were analyzed by appropriate statistical methods. RESULTS: No differences in the minor allele frequency IL-6-174G/C SNP were seen between cases and controls (0.13 vs. 0.12). The differences in the allele frequency of TNFα-308A between cases (6%) and controls (2%) have led to an odds ratio, 3.370; 95% confidence interval, 1.039-11.543; P=0.033 in the univariate analysis. In the final logistic regression analysis, however none of the variants were associated with an increased risk of CAD. CONCLUSIONS: In summary, no association of the permissive promoter variants in the IL-6 gene and the TNFα gene were seen with an increased CAD risk. These and other studies highlight the importance of doing population specific studies.

Variant on 9p21 is strongly associated with coronary artery disease but lacks association with myocardial infarction and disease severity in a population in Western India.

BACKGROUND AND AIMS: Coronary artery disease (CAD) is the leading cause of death worldwide, especially so in Indians. Recently, genome-wide studies have implicated SNPs in the 58 kb region of chromosome 9p21 to be associated with CAD. In the current study we evaluated the association of single nucleotide polymorphism (SNP) rs10757278 at the 9p21 locus with CAD in a population from Western India. METHODS: Genotyping for rs10757278 A/G was done by direct sequencing in 215 cases with confirmed CAD and 150 controls. RESULTS: A significantly higher frequency of the G allele was seen in cases as compared to controls (0.64 vs. 0.53). In the current study the G allele showed association with risk of CAD (OR 1.832 per G allele 95% 1.035-3.242, P 0.042; OR 2.452 GG vs. AA 95% 1.358-4.4431, P 0.004). Addition of the 9p21 allele to Framingham risk score (FRS) resulted in a shift of 17% of individuals from the low-risk category to the intermediate-low (>5-<10% 10-year risk) and 7% from intermediate-low to intermediate-high (>10-<20% 10-year risk) categories. CONCLUSIONS: The rs10757278 G variant at the 9p21 locus is significantly associated with the risk of CAD in our population of Western India, similar to the observed trend in other populations; however, the association is much stronger in the present cohort and, considering the high propensity of Indians to develop CAD, it is an important marker even in terms of risk classification.

Investigation of KIF6 Trp719Arg in a case-control study of coronary artery disease in Western Indians.

BACKGROUND: A single-nucleotide polymorphism Trp719Arg (rs20455T>C) in the kinesin-like protein 6 (KIF6), which is a protein involved in intracellular transport, has been shown to predict increased coronary artery disease (CAD) risk and event reduction during statin therapy. AIM: In the current study, we have evaluated the association of the variant Trp719Arg with CAD/non fatal myocardial infarction (MI) in Western Indians. METHODS: Genotyping for Trp719Arg was done by an allele-specific real-time assay in 227 cases with confirmed CAD and 150 controls. RESULTS: We have found that the KIF6 719 Arg carriers were not at a significantly higher risk for CAD/non-fatal MI in this case-control study of an Indo-European population from Western India (Unadjusted odds ratio [OR] 0.767 95% confidence interval [CI] 0.573-1.027 for 719Arg carriers). When the genotypes were further tested to determine association with prevalent myocardial infarction as the event versus CAD, no association was seen in a univariate analysis (MI vs. CAD OR 0.804 95% CI 0.543-1.189; MI vs. Controls OR 0.702 95% CI 0.482-1.021). CONCLUSION: In summary, carriers of the KIF6 719Arg allele were not at increased risk of CAD/non-fatal MI in a case-control study of Indians (Indo-Europeans) living in Western India.

Genetic variants at the APOE, lipoprotein lipase (LpL), cholesteryl ester transfer protein (CETP), and endothelial nitric oxide (eNOS) genes and coronary artery disease (CAD): CETP Taq1 B2B2 associates with lower risk of CAD in Asian Indians.

Coronary artery disease (CAD) arises due to a complex interplay between the environment and genetic factors. Alterations in many of the biomarkers such as lipids and lipoprotein levels are characteristic of CAD. The phenotypes themselves have genetic determinants, and many single-nucleotide polymorphisms (SNPs) have been identified which influence them. The current study aims to evaluate the effect of six common polymorphisms at four loci, lipoprotein lipase (D9N, N291S, S447X), apolipoprotein E (APOE), cholesteryl ester transfer protein (C277T), and endothelial nitric oxide synthase (E298D), on lipid and lipoprotein levels and its association with CAD. Genotyping for the SNPs was done in 240 Indians of which 90 had proven CAD. The other 150 were clinically free from CAD and acted as controls. Relation of genetic variants, clinical history, and biochemical parameters with CAD were analyzed by multiple regression analysis. The frequency of the B2 allele in the CETP gene was significantly lower in cases than in controls (0.40 vs 0.49, P = 0.042). Significant association of CETP Taq1B SNP was seen with total cholesterol and low density lipoprotein cholesterol. Multivariate analysis accounting for clinical and metabolic predictors of CAD showed smoking to be a significant risk factor (odds ratio (OR) 4.347, 95% confidence interval (CI) 1.888-10.012, P = 0.001) and the CETP B2 variant imparting atheroprotection (OR 0.312, 95% CI 0.116-0.841, P = 0.021) possibly through a favorable lipid profile. None of the other SNPs were associated with the risk of CAD.

Influence of genetic variants in the apolipoprotein A5 and C3 gene on lipids, lipoproteins, and its association with coronary artery disease in Indians.

Indians worldwide demonstrate a triad of elevated triglyceride (TG) with high low-density lipoprotein cholesterol and low high-density lipoprotein cholesterol levels. In the present study, we aim to investigate the effect of -1131T > C, -3A > G, c.56 C > G, and c.553 G > T SNPs in the apolipoprotein A5 (APOA5) gene and 1100C > T and 3238C > G in the apolipoprotein C3 (APOC3) on plasma lipid and lipoprotein levels and risk of coronary artery disease (CAD) in Indians. Genotyping and lipid assays were carried out using standard protocols in a study population that included 150 controls and 90 cases with CAD. Significant associations between minor alleles and higher TG levels were seen for -1131T > C (P < 0.001), -3A > G (P < 0.001), c.56C > G (P = 0.026), and c.553G > T (P = 0.003) SNPs in the APOA5 gene and 1100C > T (P = 0.001) and 3238C > G (P = 0.009) in the APOC3 gene. The haplotypes 11211, 22111, 11112, and 22112 were significantly associated with TG levels (P = 0.025, P = 0.017, P = 0.027, and P < 0.001, respectively) and very-low-density lipoprotein cholesterol levels (P = 0.025, P = 0.017, P < 0.001, and P = 0.002) in males. The 22111, 11112, and 22112 were associated with elevated TG (P = 0.030, P = 0.036, and P = 0.024) but not VLDL-C levels in females. No association with other lipid parameters was seen. In the logistic regression model, the rare S2 allele was a significant risk factor (P = 0.030, 95% CI 1.186-31.432) along with smoking (P < 0.0001, 95% CI 2.018-10.397) for CAD. The APOA5 and APOC3 locus is a strong determinant of plasma TG levels in Indians. The APOC3 3238G is a risk factor for CAD and a higher frequency was also seen with type 2 diabetes mellitus.

Mutations in the HD and PEST domain of Notch-1 receptor in T-cell acute lymphoblastic leukemia: report of novel mutations from Indian population.

Notch-1 is a transmembrane receptor protein that directs T-cell differentiation. Gain-of-function mutations in Notch-1 have been reported in more than 50% of human T-cell acute lymphoblastic leukemia (T-ALL). The current study was undertaken to characterize mutations in the heterodimerization (HD) domain and proline, glutamic acid, serine, threonine-rich (PEST) domain of the Notch-1 receptor. RNA was isolated from peripheral blood/bone marrow of 15 de novo T-ALL subjects; the Notch-1 HD and PEST regions were amplified and sequenced. Overall six patients (40%) had at least one Notch-1 mutation, 2/15 (13%) in the HD and 4/15 (27%) in the PEST domain. None of the samples showed simultaneous mutations in HD and PEST domains. Mutations were seen in 4/10 adult patients (40%); in the pediatric cohort 2/5 (40%) had mutations both of which were in the PEST domain. Of the different mutations, two have been previously reported and the other four are novel. A high incidence of Notch-1 mutations has been seen; unlike other studies, a higher frequency of mutations was found in PEST domain. The current study also served to identify four novel mutants that add new insights into the genetic heterogeneity of T-ALL. More ongoing larger studies are warranted to elucidate the molecular pathogenesis of T-ALL that arises in this part of the world.

Frequency of fokI and taqI polymorphism of vitamin D receptor gene in Indian population and its association with 25-hydroxyvitamin D levels.

BACKGROUND: The VDR protein is at the centre of the vitamin D endocrine system, a complex physiological system with substantial feedback regulatory mechanisms involved in maintaining serum calcium and 1, 25 dihydroxy vitamin D3. Variations in VDR gene are shown to have implications in several diseases and have also been implicated as an important genetic factor affecting bone mass. AIM: To determine the frequency of Fok I and Taq I variants in healthy Indian individuals and its association with 25-OH-Vitamin D levels. SETTINGS AND DESIGN: Blood samples were collected from 143 unrelated normal individuals (Male-84 and Female-59) and their genotypes determined. MATERIALS AND METHODS: After amplification by polymerase chain reaction, each polymorphism was genotyped by restriction fragment length polymorphism. For 100 normal healthy individuals 25-hydroxyvitamin D estimation was done using DiaSorin kit method. STATISTICAL ANALYSIS: Graph pad software was used to calculate the P values from the Chi-square. RESULTS: Out of 143 samples analyzed for FokI and TaqI polymorphisms the following genotypic frequency was obtained FF 59%, Ff 36%, ff 5% and TT 49%, Tt 43%, tt 8% respectively. CONCLUSIONS: Results indicate that the distribution of the polymorphic loci Fok I and Taq I vary considerably not only in different populations, but also within India. Furthermore, when the genotypes were analyzed with respect to 25-OH-Vitamin D levels, a significant association was seen for the Taq 1 SNP but not with the Fok I.