PARK2 and PARK7 Gene Polymorphisms as Risk Factors Associated with Serum Element Concentrations and Clinical Symptoms of Parkinson's Disease.

Besides clinical and imaging techniques, there is a lack of molecular makers for the diagnosis of Parkinson's disease (PD). There is an immense need to develop biomarkers associated with the phenotypes which may be valuable for individualized treatment. Single-nucleotide polymorphisms (PARK2: Ser167Asn (G>A) and Val380Leu (G>C); PARK7: IVS4 + 46G>A and IVS4 + 30T>G) in PD-related genes were examined to elucidate its relationship with concentration of serum elements and clinical symptoms of PD. A total of 214 PD patients and 213 controls from Indian population were genotyped using PCR and DNA sequencing methods. The serum element concentrations were detected and clinical symptoms were determined based on UPDRS scale and recorded at the time of sample collection. The IVS4 + 30T>G, Ser167Asn (G>A) and Val380Leu (G>C) polymorphisms appeared to alter element concentrations in PD. The patients with Ser167Asn polymorphism showed significant association with copper, iron and zinc that reinforces the role of A allele as a factor for change in the concentrations of elements, than those patients with G allele. In particular, patients with A allele of Ser167Asn have risk of having high serum iron concentration (OR 11.55, 95% CI 5.59-23.85), which are associated with dementia and postural imbalance. Similar results were observed for Val380Leu (G>C) and IVS4 + 30T>G polymorphisms which suggest their role in element concentration and neurological symptoms. Overall, our study demonstrates the influence of polymorphisms of PD genes on element concentrations and clinical symptoms. Results of this study may be taken into account when considering the contributing factors for PD symptoms.

Loss of function mutation in the P2X7, a ligand-gated ion channel gene associated with hypertrophic cardiomyopathy.

Hypertrophic cardiomyopathy (HCM) is an inherited heart failure condition, mostly found to have genetic abnormalities, and is a leading cause of sudden death in young adults. Whole exome sequencing should be given consideration as a molecular diagnostic tool to identify disease-causing mutation/s. In this study, a HCM family with multiple affected members having history of sudden death were subjected to exome sequencing along with unaffected members. Quality passed variants obtained were filtered for rarity (MAF > 0.5%), evolutionary conservation, pathogenic prediction, and segregation in affected members after removing shared variants present in unaffected members. Only one non-synonymous mutation (p. Glu186Lys or E186K) in exon 6 of P2X7 gene segregated in HCM-affected individuals which was absent in unaffected family members and 100 clinically evaluated controls. The site of the mutation is highly conserved and led to complete loss of function which is in close vicinity to ATP-binding site-forming residues, affecting ATP binding, channel gating, or both. Mutations in candidate genes which were not segregated define clinical heterogeneity within affected members. P2X7 gene is highly expressed in the heart and shows direct interaction with major candidate genes for HCM. Our results reveal a significant putative HCM causative gene, P2X7, for the first time and show that germ-line mutations in P2X7 may cause a defective phenotype, suggesting purinergic receptor involvement in heart failure mediated through arrhythmias which need further investigations to be targeted for therapeutic interventions.

Metallomic Biomarkers in Cerebrospinal fluid and Serum in patients with Parkinson's disease in Indian population.

Parkinson's disease (PD) is a neurodegenerative disease with the absence of markers for diagnosis. Several studies on PD reported the elements imbalance in biofluids as biomarkers. However, their results remained inconclusive. This study integrates metallomics, multivariate and artificial neural network (ANN) to understand element variations in CSF and serum of PD patients from the largest cohort of Indian population to solve the inconsistent results of previous studies. Also, this study is aimed to (1) ascertain a common element signature between CSF and serum. (2) Assess cross sectional element variation with clinical symptoms. (3) Develop ANN models for rapid diagnosis. A metallomic profile of 110 CSF and 530 serum samples showed significant variations in 10 elements of CSF and six in serum of patients compared to controls. Consistent variations in elements pattern were noticed for Calcium, Magnesium and Iron in both the fluids of PD, which provides feasible diagnosis from serum. Furthermore, implementing multivariate analyses showed clear classification between normal and PD in both the fluids. Also, ANN provides 99% accuracy in detection of disease from CSF and serum. Overall, our analyses demonstrate that elements profile in biofluids of PD will be useful in development of diagnostic markers for PD.

Burden among Parkinson's disease care givers for a community based study from India.

Aim was to analyze predictors of burden among primary caregivers (CGs) of Indian Parkinson's disease (PD) patients. 150 PD patients were administered using Unified Parkinson's Disease Rating Scale (UPDRS), Hoehn and Yahr Scale (H&Y), Montgomery Asberg Depression Rating Score (MADRS) and Mini Mental State Examination (MMSE) in this cross-sectional evaluation study. CG burden was assessed by Caregiver's Burden Scale (CBS), Hospital Anxiety and Depression Scale (HADS), SF-36 and 20-item Burden Assessment Schedule (BAS). Linear regression methods were used to evaluate factors contributing to burden and stress. Mean age of CG was 50.38±16.04 (range: 25-83 yrs). Marital status of CGs was noted to have significant relationship with CBS score (F=9.525, P<0.0001). Siblings (brother/sister) reported the highest CBS score while the wives reported the least. Correlations were strong between CBS and HADS anxiety (r=0.228, P=0.0048) and HADS depression (r=0.2172, P=0.0076). High correlations were found in caregiving duration, patients' stage of illness and motor disability among all the scales (CBS, HADS, SF36) determined. Step-wise regression analysis showed UPDRS (beta=1.364-0.202 ranging among all scales) and H&Y stages (beta=2.786-7.257) to have the strongest influence on CGs. CGs of patients with depression (MADRS: P=0.007 (SF36 mental) and dementia (MMSE: P=0.01) experienced greater stress. Social and financial status was disrupted in ~60% to 80% of the CGs. Motor imbalances with disability of PD patients and severity of disease are the main factors contributing to burden and stress in CGs.

Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana.

Kol, Bhil and Gond are some of the ancient tribal populations known from the Ramayana, one of the Great epics of India. Though there have been studies about their affinity based on classical and haploid genetic markers, the molecular insights of their relationship with other tribal and caste populations of extant India is expected to give more clarity about the the question of continuity vs. discontinuity. In this study, we scanned >97,000 of single nucleotide polymorphisms among three major ancient tribes mentioned in Ramayana, namely Bhil, Kol and Gond. The results obtained were then compared at inter and intra population levels with neighboring and other world populations. Using various statistical methods, our analysis suggested that the genetic architecture of these tribes (Kol and Gond) was largely similar to their surrounding tribal and caste populations, while Bhil showed closer affinity with Dravidian and Austroasiatic (Munda) speaking tribes. The haplotype based analysis revealed a massive amount of genome sharing among Bhil, Kol, Gond and with other ethnic groups of South Asian descent. On the basis of genetic component sharing among different populations, we anticipate their primary founding over the indigenous Ancestral South Indian (ASI) component has prevailed in the genepool over the last several thousand years.

Germline mutations of TP53 gene in breast cancer.

Germline alterations of the TP53 gene encoding the p53 protein have been observed in the majority of families with the Li-Fraumeni syndrome, a rare dominantly inherited disorder with breast cancer. Genomic DNA samples of 182 breast cancer cases and 186 controls were sequenced for TP53 mutations in the exon 5-9 and intervening introns 5, 7-9. Direct sequencing was done using Applied Biosystem 3730 DNA analyzer. In the present study, we observed nine mutations in the sequenced region, of which five were novel. Hardy-Weinberg equilibrium (HWE) was done for all the mutations; C14181T, T14201G, and G13203A have shown deviation from HWE. High linkage disequilibrium (LD) was observed between C14181T (rs129547788) and T14201G (rs12951053) (r (2) = 0.98.3; D' = 1.00), whereas other observed mutations do not show strong LD with any of the other mutations. None of the intronic mutations has shown significant association with the breast cancer, two exonic mutations G13203A (rs28934578) and A14572G are significantly (P = 0.04, P = 0.007) associated with breast cancer. Germline mutations observed in DNA-binding domain of the gene showed significant association with breast cancer. This study reports five novel germline mutations in the TP53 gene out of which one mutation may confer significant risk to the breast cancer. Mutations in DNA-binding domain of TP53 gene may play role in the early onset and prognosis of breast cancer. The population-based studies of germline mutations in DNA-binding domain of TP53 gene helps in identification of individuals and families who are at risk of developing cancers.

Dementia and cognitive impairment in patients with Parkinson's disease from India: a 7-year prospective study.

Depression and cognitive impairment are frequent manifestations in Parkinson's disease (PD). Although a few longitudinal studies have reported on depression and dementia in PD, there is a yet a lack of such studies in India. This 7-year longitudinal study is a hospital-based prospective case (n = 250)-control (n = 280) study. In all, 36.8% had PD with no cognitive impairment (PD-Normal), 27.2% of the patients with PD were affected by dementia (PDD), and 36% of the remaining patients with PD had mild cognitive impairment (PD-MCI) at baseline. After 7 years of evaluation, 32 new patients, 12 patients from the PD-MCI group and 9 patients from the PD-Normal group, were diagnosed with dementia. The 7-year prevalence rate for dementia was estimated to be 49.28%. In the Indian population, an early onset of dementia is noted among patients with PD, with the age of onset being less than 55 years. Patients with early-onset PDD showed depression symptoms that differed significantly from the controls of the same age-group. There was a major difference in verbal fluency, word list recall, constructional praxis and recall, word list recognition, abridged Boston Naming Test, word list memory with repetition, and Mini-Mental State Examination between PD-MCI and PDD groups. Hallucinations before baseline (odds ratio [OR] = 4.427, 95% confidence interval [CI] = 2.122-9.373), akinetic/tremor dominancy (OR = 0.380, 95%CI = 0.149-0.953), and asymmetrical disease onset (OR = 0.3285, 95%CI = 0.1576-0.685) can be considered as risk factors for patients with dementia. Patients with early-onset PD might be more prone to complex depression and dementia. As the disease progresses, akinetic-dominant PD, early hallucinations, and asymmetrical disease onset are the potential risk factors for the development of dementia in patients with PD.

Role of HLA class II loci polymorphism in the manifestation of type 1 diabetes in a Bengali Indian patient population.

To assess the contribution of the HLA class II region for susceptibility to type 1 diabetes mellitus (T1DM), we investigated the association of HLA class II alleles-DP, DQ, and DRB1. Here, we present an extensive molecular typing for HLA class II alleles and their haplotypes in a Bengali-speaking Indian population of T1DM patients (n=151) and controls (n=151) from West Bengal. HLA typing was done by DNA sequencing using a 3730 DNA Analyzer. The individual analysis of each gene gave the following alleles to be higher in cases than in controls, thus making them susceptible alleles-DPA1*020103, DPB1*020102, DQA1*050101, DQA1*0201, and DQB1*020101G. Similarly, the following alleles are protective alleles in our study-DPA1*010602, DPB1*040101, DQA1*010201, DQA1*0103, and DRB1*15. Our result confidently establishes that HLA-DP allelic, and its haplotypic, diversity contributes significantly to the risk for T1DM. The DQA1*0103 allele is a novel allele with a significant association with the protection from T1DM. Among the various haplotypes tested, the DQA1*0201:DQB1*020101G, DQA1*050101:DQB1*020101G, and DQA1*0201:DQB1*030101G were the most frequently found in T1DM patients. In India, very few investigations have been undertaken to study the impact of the genetic background on the risk to develop T1DM in its population, where the annual average incidence is 10.5/100,000/year. In conclusion, the present study highlights the genetic effect of HLA haplotypes that contributes to the susceptibility to T1DM.

Association of TCF7L2 and ADIPOQ with body mass index, waist-hip ratio, and systolic blood pressure in an endogamous ethnic group of India.

Despite the increasing burden of type 2 diabetes (T2D) and its established association with anthropometric and physiological traits as a risk factor, genetic studies focusing on the association of T2D-related genes with quantitative traits like body mass index (BMI), waist-hip ratio (WHR), and systolic blood pressure (SBP) are only a few for western populations and rare for Indian populations. The present study tested the association of TCF7L2, HHEX, KCNJ11, and ADIPOQ with BMI, SBP, and WHR in men and women of the Aggarwal population of India and found a differential association of TCF7L2 (rs7903146, rs4506565, and rs12256372) and ADIPOQ (rs2241766 and rs1501299) genes with increasing BMI, SBP, and WHR between the two sexes. We conclude that TCF7L2 and ADIPOQ together might play an important role in explaining these traits and to understand the biological and genetic mechanisms underlying T2D, and the role of other T2D genes must also be evaluated with these continuous traits.

Population structure of Aggarwals of north India as revealed by molecular markers.

Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.

A validation study of type 2 diabetes-related variants of the TCF7L2, HHEX, KCNJ11, and ADIPOQ genes in one endogamous ethnic group of north India.

The aim of this study was to validate the single nucleotide polymorphisms (SNPs) of four candidate genes (TCF7L2, HHEX, KCNJ11, and ADIPOQ) related to type 2 diabetes (T2D) in an endogamous population of north India; the Aggarwal population, having 18-clans. This endogamous population model was heavily supported by recent land mark work and we also verified the homogeneity of this population by clan-based stratification analysis. Two SNPs (rs4506565; rs7903146) in TCF7L2 were found to be significant (p-value = 0.00191; p-value = 0.00179, respectively), and odds ratios of 2.1 (dominant-model) and 2.0 (recessive-model) respectively, were obtained for this population. The TTT haplotype in the TCF7L2 gene was significantly associated with T2D. Waist-Hip ratio (WHR), systolic blood pressure (SBP), and age were significant covariates for increasing risk of T2D. Single-SNP, combined-SNPs and haplotype analysis provides clear evidence that the causal mutation is near to or within the significant haplotype (TTT) of the TCF7L2 gene. In spite of a culturally-learned sedentary lifestyle and fat-enriched dietary habits, WHR rather than body-mass-index emerged as a robust predictor of risk for T2D in this population.

Cross-sectional reference values of upper arm anthropometry of the Khasi tribal adolescents of Meghalaya, India.

The Khasi tribal people in India with their distinct ethnic identity have relative geographic isolation from the rest of the country. Although chronic energy deficiency has been documented in this population, their nutritional status has not been re-evaluated following a decade of economic growth in India. In this study, the nutritional status of an ethno-homogenous sample of contemporary Khasi tribal adolescent cohort of age 11+ to 17+ years in the state of Meghalaya, India has been assessed by cross sectional analysis. This was achieved through the use of the following derived anthropometric measurements - total upper arm area (TUA), upper arm muscle area (UMA), upper arm fat area (UFA), and arm fat index (AFI). A total of 670 adolescents (335 boys; 335 girls) participated in this study. In comparison with North American NHANES 1999-2002 standards, UMA, a measure of upper arm muscle mass, was lower at all age groups in Khasi girls. Conversely, in Khasi boys, AFI, a marker of upper arm fat mass was lower at all age groups, thereby showing a gender dimorphic difference in upper limb muscle and fat proportions. We conclude that in upper arm indirect anthropometry, contemporary Khasi adolescent children remain nutritionally deficient with gender dimorphic muscle and fat proportions.

Updating phylogeny of mitochondrial DNA macrohaplogroup m in India: dispersal of modern human in South Asian corridor.

To construct maternal phylogeny and prehistoric dispersals of modern human being in the Indian sub continent, a diverse subset of 641 complete mitochondrial DNA (mtDNA) genomes belonging to macrohaplogroup M was chosen from a total collection of 2,783 control-region sequences, sampled from 26 selected tribal populations of India. On the basis of complete mtDNA sequencing, we identified 12 new haplogroups--M53 to M64; redefined/ascertained and characterized haplogroups M2, M3, M4, M5, M6, M8'C'Z, M9, M10, M11, M12-G, D, M18, M30, M33, M35, M37, M38, M39, M40, M41, M43, M45 and M49, which were previously described by control and/or coding-region polymorphisms. Our results indicate that the mtDNA lineages reported in the present study (except East Asian lineages M8'C'Z, M9, M10, M11, M12-G, D) are restricted to Indian region.The deep rooted lineages of macrohaplogroup 'M' suggest in-situ origin of these haplogroups in India. Most of these deep rooting lineages are represented by multiple ethnic/linguist groups of India. Hierarchical analysis of molecular variation (AMOVA) shows substantial subdivisions among the tribes of India (Fst = 0.16164). The current Indian mtDNA gene pool was shaped by the initial settlers and was galvanized by minor events of gene flow from the east and west to the restricted zones. Northeast Indian mtDNA pool harbors region specific lineages, other Indian lineages and East Asian lineages. We also suggest the establishment of an East Asian gene in North East India through admixture rather than replacement.

Dopamine transporter (DAT1) VNTR polymorphism in 12 Indian populations.

The dopamine transporter (DAT1) is a membrane spanning protein that binds the neurotransmitter dopamine and performs re-uptake of dopamine from the synapse into a neuron. The gene encoding DAT1 consists of 15 exons spanning 60 kb on chromosome 5p15.32. Several studies have investigated the possible associations between variants in DAT1 gene and psychiatric disorders. The present study aimed to determine the distribution of the variable number of tandem repeat (VNTR) polymorphism in the 3' untranslated region of DAT1 in 12 Indian populations. A total of 471 healthy unrelated individuals in 12 Indian populations from 3 linguistic groups were included in the present study. The analysis was carried out using PCR and electrophoresis. Overall, 4 alleles of the DAT1 40-bp VNTR, ranging from 7 to 11 repeats were detected. Heterozygosity indices were low and varied from 0.114 to 0.406. The results demonstrate the variability of the DAT1 40-bp VNTR polymorphism in Indian populations and revealed a high similarity with East Asian populations.