Papers by Partha Majumder
Additional file 3: Table S3. Significantly enriched GO terms in OSCC-GB patients based on 209 gen... more Additional file 3: Table S3. Significantly enriched GO terms in OSCC-GB patients based on 209 genes significantly differentially methylated in their promoter regions and related information.
Human Genetics, 2000
To identify various subtypes of spinocerebellar ataxias (SCAs) among 57 unrelated individuals cli... more To identify various subtypes of spinocerebellar ataxias (SCAs) among 57 unrelated individuals clinically diagnosed as ataxia patients we analysed the SCA1, SCA2, SCA3, SCA6, SCA7 and DRPLA loci for expansion of CAG repeats. We detected CAG repeat expansion in 6 patients (10.5%) at the SCA1 locus. Ten of the 57 patients (17.5%) had CAG repeat expansion at the SCA2 locus, while four had CAG expansion at the SCA3/MJD locus (7%). At the SCA6 locus there was a single patient (1.8%) with 21 CAG repeats. We have not detected any patient with expansion in the SCA7 and DRPLA loci. To test whether the frequencies of the large normal alleles in SCA1, SCA2 and SCA6 loci can reflect some light on prevalence of the subtypes of SCAs we studied the CAG repeat variation in these loci in nine ethnic sub-populations of eastern India from which the patients originated. We report here that the frequency of large normal alleles (>31 CAG repeats) in SCA1 locus to be 0.211 of 394 chromosomes studied. We also report that the frequency of large normal alleles (>22 CAG repeats) at the SCA2 locus is 0.038 while at the SCA6 locus frequency of large normal alleles (>13 repeats) is 0.032. We discussed our data in light of the distribution of normal alleles and prevalence of SCAs in the Japanese and white populations.
Human Genetics, 2001
The frequencies of haplotypes based upon the (CTG) n repeat and three other biallelic markers in ... more The frequencies of haplotypes based upon the (CTG) n repeat and three other biallelic markers in and around the myotonic dystrophy (DM) locus were estimated in 13 ethnically, linguistically and geographically diverse sub-populations of India. The range of CTG repeats in caste populations was 5-31, while in tribal populations the range was shorter (5-23). Extensive variation in frequencies of large (CTG) n alleles (≥18 repeats) was found in Indian populations. The implications of this finding on DM epidemiology are discussed. Haplotype diversity was found to be very high in most populations. The majority of the Indian DM patients carried a haplotype that is commonly found among DM patients globally; this is the most common haplotype in the class of large (≥18 repeats) CTG alleles. However, one haplotype was found to be present in particularly high frequency in Indian populations; this haplotype was also found among Indian DM patients. This haplotype may be a characteristic of Indian and possibly of other East Asian populations.
Genetic Epidemiology, 1989
Several studies have reported association between noninsulin-dependent diabetes mellitus and GC, ... more Several studies have reported association between noninsulin-dependent diabetes mellitus and GC, the vitamin D binding protein of human plasma, with the GC 1 allele in significant excess among diabetics. Additionally, there is a considerable body of animal data suggesting that vitamin D has a significant impact on insulin secretion. Examination of the insulin levels in Dogrib Indians showed that the lowest levels of fasting insulin were associated with the GC IF-IF genotype. The present study examined levels of glucose, C-peptide, and insulin at fasting and 1 hr and 2 hr following a 75 g oral glucose challenge, in a population of Hispanic-Americans and Anglos in the San Luis Valley of southern Colorado. The sample comprised a total of 468 individuals with normal glucose tolerance. Of these, 289 were Anglos and 179 were Hispanic-Americans. An analysis of covariance was performed to determine the effect of the GC genotypes on mean levels of the primary variables--glucose, C-peptide, and insulin--and a secondary variable--insulinogenic index adjusting for the covariates age, body mass index (BMI), gender, and ethnicity. The analyses revealed that there is a significant difference in mean levels of glucose at fasting (F value = 2.46; P = 0.033) among the GC genotypes in the sample. Additionally, the differences in mean levels of 1 hr postprandial glucose among the GC genotypes although not significant at a 5% level, were significant at the 10% level. No other significant phenotypic effects were observed. These analyses are not in concordance with the results of an earlier study, where lower fasting insulin was associated with the GC 1F-1F genotype.
Genetic Epidemiology, 1985
An epidemiological profile of vitiligo in Calcutta is presented. Prevalence data were gathered fr... more An epidemiological profile of vitiligo in Calcutta is presented. Prevalence data were gathered from 15,685 individuals drawn from the general population; pedigree data were collected through 293 vitiligo patients. The overall prevalence of vitiligo is about 5 per 1,000 individuals. There are no significant sex or age differences in prevalence rates. About a 4.5-fold increase in prevalence is observed among close biological relatives of affected individuals. There is, however, no clearcut correspondence between relative risks and kinship coefficients. There are no significant differences in the frequencies of various types of vitiligo between probands with and without positive family history. The overall mean and modal ages of onset are about 22 years and 15 years, respectively. The mean ages among males (24.8 years) and females (19.3 years) are significantly different.
Scientific Reports, 2016
The skin microbiome varies across individuals. The causes of these variations are inadequately un... more The skin microbiome varies across individuals. The causes of these variations are inadequately understood. We tested the hypothesis that inter-individual variation in facial skin microbiome can be significantly explained by variation in sebum and hydration levels in specific facial regions of humans. We measured sebum and hydration from forehead and cheek regions of healthy female volunteers (n = 30). Metagenomic DNA from skin swabs were sequenced for V3-V5 regions of 16S rRNA gene. Altogether, 34 phyla were identified; predominantly Actinobacteria (66.3%), Firmicutes (17.7%), Proteobacteria (13.1%) and Bacteroidetes (1.4%). About 1000 genera were identified; predominantly Propionibacterium (58.6%), Staphylococcus (8.6%), Streptococcus (4.0%), Corynebacterium (3.6%) and Paracoccus (3.3%). A subset (n = 24) of individuals were sampled two months later. Stepwise multiple regression analysis showed that cheek sebum level was the most significant predictor of microbiome composition and ...
Annals of Human Biology, 1984
The theoretical justifications for using the number of rare alleles observed in a sample and the ... more The theoretical justifications for using the number of rare alleles observed in a sample and the heterozygosity contributed by such alleles to estimate the relative electrophoretic mutation rate (REMR) are given in this note. It is shown that the estimator using the number of alleles has comparatively less bias. While the total heterozygosity contributed by all alleles at a locus has been previously used to estimate REMR with success, an analogous estimator with only rare alleles has large bias over a wide range of effective population size and sample size.
Investigative ophthalmology & visual science, 2006
To obtain a global perspective on the distribution and evolution of CYP1B1 mutations in primary c... more To obtain a global perspective on the distribution and evolution of CYP1B1 mutations in primary congenital glaucoma (PCG) worldwide. Five intragenic single-nucleotide polymorphisms in CYP1B1-R48G, A119S, V432L, D449D, and N453S-were used to generate haplotype data from 138 Indian patients with PCG and 132 ethnically matched normal controls, which were then analyzed in conjunction with data from other populations. Maximum-likelihood estimates of haplotype frequencies were estimated from the genotype data. Subsets of patients and normal control subjects were also genotyped with respect to eight short tandem repeat (STR) markers around the CYP1B1 locus (D2S305, D2S165, D2S367, D2S2259, D2S391, D2S3337, D2S23678, and D2S286), to gain evolutionary insights. Common mutations in CYP1B1 that are causal of PCG occurred on a uniform haplotype background among Indian patients, which is completely distinct from the modal haplotype background found among unaffected control subjects. Comparison o...
Journal of Child Psychology and Psychiatry, 1998
This study aims to identify (1) a core disruptive behavior disorder (DBD) postulated to presage a... more This study aims to identify (1) a core disruptive behavior disorder (DBD) postulated to presage a substance use disorder, and (2) the relative importance of parental DBD phenotypes, and familial and nonfamilial environmental factors in the determination of DBD in male children. DBD symptom counts and measures of familial and nonfamilial environmentals were collected from intact families ascertained through the presence (SA+) or absence (SA-) of substance dependence in fathers. Multivariate analyses revealed that both behavioral symptoms and environmental measures were significant discriminators of the families. In SA+ families, the child's score DBD was best predicted by magnitudes of parental dyssocial behaviors and by familial environmental factors. However, in SA- families only familial environmental factors were significant predictors of the child's DBD. These findings suggest that in addition to independent actions of familial transmissible and nonfamilial factors, strong genotype-environment interactions may determine DBD in children and that may contribute to the liability for a substance use disorder.
European Journal of Human Genetics, 1999
DNA samples from 396 unrelated individuals belonging to 14 ethnic populations of India, inhabitin... more DNA samples from 396 unrelated individuals belonging to 14 ethnic populations of India, inhabiting various geographical locations and occupying various positions in the socio-cultural hierarchy, were analysed in respect of 8 human-specific polymorphic insertion/deletion loci. All loci, except Alu CD4, were found to be highly polymorphic in all populations. The levels of average heterozygosities were found to be very high in all populations and, in most populations, also higher than those predicted by the island model of population structure. The coefficient of gene differentiation among Indian populations was found to be higher than populations in most other global regions, except Africa. These results are discussed in the light of two possible scenarios of evolution of Indian populations in the broader context of human evolution.
Background: Studies of epigenomic alterations associated with diseases primarily focus on methyla... more Background: Studies of epigenomic alterations associated with diseases primarily focus on methylation profiles of promoter regions of genes, but not of other genomic regions. In our past work (Das et al. 2019) on patients suffering from gingivo-buccal oral cancer – the most prevalent form of cancer among males in India – we have also focused on promoter methylation changes and resultant impact on transcription profiles. Here, we have investigated alterations in non-promoter (gene-body) methylation profiles and have carried out an integrative analysis of gene-body methylation and transcriptomic data of oral cancer patients. Methods: Tumor and adjacent normal tissue samples were collected from 40 patients. Data on methylation in the non-promoter (gene-body) regions of genes and transcriptome profiles were generated and analyzed. Because of high dimensionality and highly correlated nature of these data, we have used Random Forest (RF) and other data-analytical methods.Results: Our inte...
The Human Cell Atlas has been undergoing a massive effort to support global scientific equity. Th... more The Human Cell Atlas has been undergoing a massive effort to support global scientific equity. The co-leaders of its Equity Working Group share some lessons learned in the process.
We thank HCA Organizing Committee members Dana Pe'er, Gary Bader and Henk Stunnenberg for multipl... more We thank HCA Organizing Committee members Dana Pe'er, Gary Bader and Henk Stunnenberg for multiple critical readings of the entire white paper and their insightful comments.
The FASEB Journal, 2014
Background and Objective: Variations in the cytochrome P450, family 1, subfamily B, polypeptide 1... more Background and Objective: Variations in the cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) gene and mutations in the latent transforming growth factor beta binding protein 2 (LTBP2) gene cause autosomal recessive Primary Congenital Glaucoma (PCG). However, in India, only 45% of PCG patients harbor alterations in the CYP1B1 gene. The present study aimed to identify novel genetic variations contributing to unexplained PCG cases in India. Methods: 112 unrelated Indian PCG patients in whom neither chromosome carried a CYP1B1 or an LTBP2 mutation, and 106 matched controls, were recruited for this study. DNA isolated from each case and control was screened for a total of 906,600 single nucleotide polymorphism (SNP) loci using an Affymetrix 6.0 whole genome genotyping array. The marker data were first used for an association analysis followed by multiple test corrections, after an initial adjustment for population stratification. A second approach undertaken in this study was detection of regions...
Additional file 1: Table S1. Relevant details of 209 genes with significant negative correlation ... more Additional file 1: Table S1. Relevant details of 209 genes with significant negative correlation between promoter methylation and gene expression.
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Papers by Partha Majumder