PARTHA P. MAJUMDER
Articles written in Journal of Genetics
Volume 71 Issue 3 December 1992 pp 89-103
A genetic model is discussed for recessively inherited disorders that do not follow a single-locus Mendelian pattern of inheritance. Further complexity arising from variable age of onset is also discussed. Methods of statistical analysis of family data using the likelihood principle are described for such complex disorders. The methods are exemplified using data on families of prelingual deafness and vitiligo.
Volume 72 Issue 2-3 December 1993 pp 103-104 Book Review
Volume 74 Issue 1-2 April 1995 pp 41-46
Vitiligo is a dermatological disorder in man that shows familial aggregation. We performed segregation analysis on data pertaining to vitiligo on members of 147 pedigrees each ascertained through a single proband, and tested various non-genetic, and one-locus and two-locus genetic models. Non-genetic and one-locus genetic models were rejected in favour of a two-locus model postulating epistatic interaction of recessive alleles in the aetiology of vitiligo. The present results show that vitiligo is not a single-locus disorder and substantiate our earlier inference, drawn on the basis of nuclear-family data, of multilocus involvement in the pathogenesis of vitiligo.
Volume 76 Issue 3 December 1997 pp 181-188
Because microsatellite loci are abundant in the human genome and are highly polymorphic in most global populations, such loci have become very popular in studies on reconstructing evolutionary relationships among contemporary human populations. We have made an assessment of the efficiency of recovery of true evolutionary relationships using simulated data of microsatellite loci and a variety of distance measures. We find that allele frequency data on about 30 microsatellite loci and the use of
Volume 79 Issue 2 August 2000 pp 41-46
The central Indian state of Madhya Pradesh is home to a large number of tribal populations of diverse linguistic and ethnic backgrounds. With a view to examining how well genomic affinities among tribal populations of this state correspond with their ethnic and linguistic affinities, we analysed DNA samples of individuals drawn from five tribes with diverse, but reasonably well-documented, ethnohistorical and linguistic backgrounds. Each DNA sample was scored at 16 biallelic DNA marker loci. On the basis of these data, genomic affinities among these populations were estimated. We have found an extremely good correspondence between the genomic and ethnolinguistic affinities.
Volume 79 Issue 2 August 2000 pp 47-53
Mapping a locus controlling a quantitative genetic trait (e.g. blood pressure) to a specific genomic region is of considerable contemporary interest. Data on the quantitative trait under consideration and several codominant genetic markers with known genomic locations are collected from members of families and statistically analysed to estimate the recombination fraction, θ, between the putative quantitative trait locus and a genetic marker. One of the major complications in estimating θ for a quantitative trait in humans is the lack of haplotype information on members of families. We have devised a computationally simple two-stage method of estimation of θ in the absence of haplotypic information using the expectation-maximization (EM) algorithm. In the first stage, parameters of the quantitative trait locus (QTL) are estimated on the basis of data of a sample of unrelated individuals and a Bayes’s rule is used to classify each parent into a QTL genotypic class. In the second stage, we have proposed an EM algorithm for obtaining the maximum-likelihood estimate of θ based on data of informative families (which are identified upon inferring parental QTL genotypes performed in the first stage). The purpose of this paper is to investigate whether, instead of using genotypically ‘classified’ data of parents, the use of posterior probabilities of QT genotypes of parents at the second stage yields better estimators. We show, using simulated data, that the proposed procedure using posterior probabilities is statistically more efficient than our earlier classification procedure, although it is computationally heavier.
Volume 80 Issue 3 December 2001 pp 125-135
Linguistic evidence suggests that West Asia and Central Asia have been the two major geographical sources of genes in the contemporary Indian gene pool. To test the nature and extent of similarities in the gene pools of these regions we have collected DNA samples from four ethnic populations of northern India, and have screened these samples for a set of 18 Y-chromosome polymorphic markers (12 unique event polymorphisms and six short tandem repeats). These data from Indian populations have been analysed in conjunction with published data from several West Asian and Central Asian populations. Our analyses have revealed traces of population movement from Central Asia and West Asia into India. Two haplogroups, HG-3 and HG-9, which are known to have arisen in the Central Asian region, are found in reasonably high frequencies (41.7% and 14.3% respectively) in the study populations. The ages estimated for these two haplogroups are less in the Indian populations than those estimated from data on Middle Eastern populations. A neighbour-joining tree based on Y-haplogroup frequencies shows that the North Indians are genetically placed between the West Asian and Central Asian populations. This is consistent with gene flow from West Asia and Central Asia into India.
Volume 82 Issue 1-2 April 2003 pp 7-12
We have compared two statistical methods of estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences, which have been proposed by Templeton (1993) and Bandelt
Volume 83 Issue 1 April 2004 pp 101-105 Obituary
Volume 86 Issue 3 December 2007 pp 225-239 Research Article
We have studied DNA sequence variation in and around the genes
Volume 90 Issue 2 August 2011 pp 323-326 Research Note
Volume 94 Issue 1 March 2015 pp 105-113 Research Article
Nonalcoholic fatty liver disease (NAFLD) is a distinct pathologic condition characterized by a disease spectrum ranging from simple steatosis to steato-hepatitis, cirrhosis and hepatocellular carcinoma. Prevalence of NAFLD varies in different ethnic groups, ranging from 12% in Chinese to 45% in Hispanics. Among Indian populations, the diversity in prevalence is high, ranging from 9% in rural populations to 32% in urban populations, with geographic differences as well. Here, we wished to find out if this difference is reflected in their genetic makeup. To date, several candidate genes and a few genomewide association studies (GWAS) have been carried out, and many associations between single nucleotide polymorphisms (SNPs) and NAFLD have been observed. In this study, the risk allele frequencies (RAFs) of NAFLD-associated SNPs in 20 Indian ethnic populations (376 individuals) were analysed. We used two different measures for calculating genetic risk scores and compared their performance. The correlation of additive risk scores of NAFLD for three Hapmap populations with their weighted mean prevalence was found to be high (𝑅2 = 0.93). Later we used this method to compare NAFLD risk among ethnic Indian populations. Based on our observation, the Indian caste populations have high risk scores compared to Caucasians, who are often used as surrogate and similar to Indian caste population in disease gene association studies, and is significantly higher than the Indian tribal populations.
Volume 95 Issue 3 September 2016 pp 587-593 RESEARCH ARTICLE
Study of temporal trajectory of gene expression is important. RNA sequencing is popular in genome-scale studies of transcription. Because of high expenses involved, many time-course RNA sequencing studies are challenged by inadequacy of sample sizes. This poses difficulties in conducting formal statistical tests of significance of null hypotheses. We propose a bootstrap algorithm to identify ‘cognizable’ ‘time-trends’ of gene expression. Properties of the proposed algorithm are derived using a simulation study. The proposed algorithm captured known ‘time-trends’ in the simulated data with a high probability of success, even when sample sizes were small (n<10). The proposed statistical method is efficient and robust to capture ‘cognizable’ ‘time-trends’ in RNA sequencing data.
Volume 96 Issue 5 November 2017 pp 717-717 Haldane at 125
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