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Biomedical subjects

R Chakraborty

Publications and source records attributed to R Chakraborty.

At least 307 records · Page 17Linked to original sources
PubMedDate not supplied

Relative risks of diseases in the presence of incomplete penetrance and sporadics.

In most diseases of contemporary interest to epidemiology, the importance of familial risk factors is often assessed by relative risk measures computed from family history data. In this paper, we examine the efficiency of relative risk measures in discerning the genetic background of a disease. It is shown that even for a simple (one locus, two alleles) genetic disease, incomplete penetrance of the disease allele and/or occurrence of sporadics (i.e. non-heritable cases caused by environmental risk factors) often yields a rather small value of relative risk. This means that a small value of relative risk need not necessarily imply that genetic factors are unimportant in the aetiology of the disease. Furthermore, it is shown that the relative risk measures are complicated functions of disease gene frequency, the penetrance parameter and the sporadic rate. A rejection of genetic involvement for a disease on the basis of a single relative risk estimate may, therefore, be erroneous.

Genetic Diseases, Inborn↗
PubMedDate not supplied

Non-random sampling in human genetics: estimation of familial correlations, model testing, and interpretation.

By choice or necessity, human geneticists and genetic epidemiologists often design studies that involve non-random sampling of clusters of individuals, and yet address hypotheses appropriate to the population as a whole. Failure to adjust for the non-randomness of data often leads to biased parameter estimates and misspecification of predictive models that cause familial resemblance of traits. We develop an approach to adjust for common forms of non-randomness in the context of estimating familial correlation with minimal distributional assumptions and discuss its implications in connection with adjustments for concomitant variables.

Analysis of Variance↗
PubMedDate not supplied

The C677T polymorphism of the methylenetetrahydrofolate reductase gene in Mexican mestizo neural-tube defect parents, control mestizo and native populations.

The C677T mutation of the methylenetetrahydrofolate reductase (MTHFR) gene, associated with the thermolabile form of the enzyme, has reportedly been found to be increased in neural-tube defects (NTD), though this association is still unclear. A group of 107 mestizo parents of NTD children and five control populations: 101 mestizo (M), 50 Huichol (H), 38 Tarahumara (T), 21 Purepecha (P) and 20 Caucasian (C) individuals were typed for the MTHFR C677T variant by the PCR/RFLP (HinfI) method. Genotype frequencies were in agreement with the Hardy-Weinberg expectations in all six populations. Allele frequency (%) of the C677T variant was 45 in NTD, 44 in M, 56 in H, 36 in T, 57 in P, 35 in C. Pairwise inter-population comparisons of allele frequency disclosed a very similar distribution between NTD and M groups (exact test, P=0.92). Among controls, differences between M and individual native groups were NS (0.06<P<0.21), as it was between M and C (P=0.29). A high frequency of the variant was found in H (56%) and P (57%). A similar allele frequency in groups M and NTD does not support a causal relationship between NTD and parental MTHFR C677T genotypes. Thus, the C677T variant cannot be regarded as a major genetic risk factor for NTD in Mexican mestizo parents. Otherwise, C677T in Mexico is very frequent, especially in Huichol and Purepecha natives, as compared with other groups world wide.

DNA↗
PubMedDate not supplied

Estimation of mutation rates from the number of rare alleles in a sample.

To estimate the mutation rate from rare electrophoretic variants, a revised estimating equation is derived that takes into account the sampling distribution of the observed number of rare alleles in a sample drawn from the population. A check of the approximations used here suggests that the derived estimating equation is superior to the currently available one that is based on the expected number of rare alleles in the population. The new method is illustrated with a collation of electrophoretic data from literature. It is shown that the assumptions made in the theoretical treatment do not affect the estimate, per se, when the observed number of rare alleles is chosen as a statistic for estimating the mutation rates.

Alleles↗
PubMedDate not supplied

Distribution of the number of heterozygous loci in the Kota population of Nilgiri hills of India and estimation of average heterozygosity.

From an electrophoretic survey of 17 protein enzyme loci in seven Kota villages of the Nilgiri Hills, Madras region of South India, the distribution of the number of heterozygous loci is computed. It is demonstrated that the mean of this distribution provides an alternative estimate of the average heterozygosity in an individual per locus which does not make use of the assumptions of linkage equilibrium and random mating. Since the Kotas practise a high degree of consanguineous marriages, this new estimate is suggested to be more appropriate for such isolated populations. Through an FST analysis it is shown that there is very little gene differentiation among the seven Kota villages where substantial gene migration occurs through inter-village marriages.

Blood Proteins↗
PubMedDate not supplied

Genetic components of variations of red cell glycolytic intermediates at two altitudes among the South American Aymara.

Red cell haemoglobin (Hb), haematocrit (Ht), 2,3-diphosphoglycerate (DPG), and adenosine triphosphate (ATP) levels were measured in 876 individuals from six villages at two altitude levels (altiplano and coast) of the Departmento de Arica of Northern Chile. Of these, data on 761 individuals are subjected to analysis to search for the evidence of genetic adaptation to a hypoxic environment at a high altitude. Total phenotypic variance for each of the variables is higher at the altiplano as compared to their counterparts at the coastal level. Data on 1127 pairs of relatives of six degrees of relationships are used to determine the genetic component of variation in each of these four traits. To a certain extent the larger familial correlations as well as higher variances at altiplano are explained by the apparent assortative mating (which may again be due to their restricted population size) at the higher elevation. Yet, at least in three variables (Hb, Ht, and DPG) no reduction in the additive genetic component of variation is noticed at the higher altitude. ATP seems to have the highest degree of genetic component of variance, particularly at the coastal level. Some implications of these results are discussed in the light of their roles in the glycolytic pathway.

2,3-Diphosphoglycerate↗
PubMedDate not supplied

Estimation of relative electrophoretic mutation rates from rare alleles in a sample.

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.

Alleles↗
PubMedDate not supplied

Immunoglobulin (Gm and Km) allotypes in the Aymara of Chile and Bolivia.

Immunoglobulin (Gm and Km) allotype and haplotype frequencies are presented for 1707 individuals from Northern Chile and Western Bolivia, subdividing them by ethnicity and altitude of residence. The haplotype distribution of Gm as well as Km loci in these populations suggest that in almost all of the ethnicity x altitude subdivisions of this population considerable admixture of Amerindian and Caucasian genes have occurred. The haplotype frequency heterogeneity and the analysis of departure from Hardy-Weinberg expectations demonstrate that while some local variation in haplotype frequencies at the Gm and Km loci exists in this region, there is no clear evidence suggesting that the pattern of variation is due to an adaptation to the hypoxia of altitude. We conclude that such differences in haplotype frequencies are probably due to random genetic drift and differential admixture of Amerindian and Caucasian genes that have occurred in the past.

Bolivia↗
PubMedDate not supplied

Immunoglobulin (Gm and Km) allotypes in nine endogamous groups of West Bengal, India.

Blood samples from 898 individuals of nine endogamous groups of West Bengal, India were typed for determining the haplotypic structure in the gamma-light chain (Gm) and kappa-light chain (Km) of immunoglobulin (IgG). The Gm haplotype frequencies detected by Glm (1), Glm (2) and G3m (5) markers suggest that in this eastern state of India there is considerable variation of frequencies of the typical Mongoloid haplotype Gm1,5, which shows a high incidence in Rajbanshi, Rabha, Garo and Lodha groups. On the contrary, this haplotype is probably absent in the high caste groups, Rarhi Brahmin and Vaidya, and is relatively infrequent in Jalia Kaibarta, a scheduled caste of the south-western part of the state. The Km1 allele is also high in frequency among Rajbanshi, Rabha, Garo and Munda in comparison with Rarhi Brahmin and Vaidya, suggesting the former four groups' strong Mongoloid affiliation. This survey signifies that there is considerable variation in the extent of Mongoloid admixture in Bengali populations. Such admixture is not restricted in specific social class either. It further demonstrates that heterogeneity of the genetic structure of Bengali populations do not correspond to the present social ranking on the basis of caste hierarchy.

Asian People↗
PubMedDate not supplied

Gene diversity and estimation of genetic admixture among Mexican-Americans of Starr County, Texas.

The Mexican-Americans of Starr County, Texas, classified by sex and birthplace, were studied to determine the extent of genetic variation and contributions from ancestral populations such as Spanish, Amerindian and West African. Using 21 genetic marker systems, genetic distance and diversity analyses indicate that subpopulations of Mexican-Americans in Starr County are similar, and that more than 99% of the total gene diversity (HT) can be attributed to individual variation within the population. Genetic admixture analysis shows the predominant influence comes from the Spanish, a lesser contribution from Amerindians and a slight one from the West Africans. The contribution of the ancestral population to various subpopulations of the Mexican-Americans of Starr County is similar. The Mexican-Americans of Starr County are similar to the Mexican population from northeastern Mexico. The history of admixture is apparently old enough to have brought the entire Mexican-American gene pool to Hardy-Weinberg equilibrium. There is no non-random association of alleles among the genetic marker systems considered in the present study, in spite of the fact that this population is of admixed origin. These results, in aggregate, suggest genetic homogeneity of the Mexican-Americans of Starr County, Texas, and point towards the utility of this population for genetic and epidemiological studies.

Africa↗