Biomedical subjects

R Chakraborty

Publications and source records attributed to R Chakraborty.

At least 91 records · Page 5Linked to original sources

PubMed1996

Measures of variation at DNA repeat loci under a general stepwise mutation model.

Polymorphisms at tandem repeat loci are caused by mutations with allele sizes occasionally altered by more than one repeat unit in both forward and backward directions. Such mutational changes may occur with asymmetric probabilities. Therefore, a one-step symmetric stepwise mutation model may not be appropriate for studying the population dynamics at all repeat loci. In this work, we evaluated the expectation and variance of the within-population variance of the allele size distribution in a finite population, and the expected homozygosity at a locus by the coalescence approach under a general stepwise mutation model, where mutational transitions of allele sizes can be arbitrary, including being asymmetric. Under the special cases of symmetric one-step, two-step, and multi-step geometric distributions of mutations, our general results reduce to the corresponding results obtained by earlier investigators. The general results indicate that in a finite population, which has reached a steady state under the (general stepwise) mutation and drift balance, the within-population variance of allele sizes has a simple expectation (i.e., proportional to Nnu, the product of the mutation rate, nu, and effective population size, N). However, its stochastic variance is a quadratic function of this composite parameter, Nnu. Furthermore, this second-order variance does not decay with the number of alleles sampled from a population. Application of this theory to data on allele size distributions in unrelated Caucasians from the CEPH pedigree (obtained from the Genome Data Base) shows that the relationship of the variance and mean of within-population variance of allele sizes at tandem repeat loci, grouped by their chromosomal assignment, has a trend compatible with the theory. However, there is an indication that the second-order variance is generally underestimated. One reason for this departure might be that the CEPH sample may not represent a single homogeneous population that reached equilibrium at all tandem repeat loci.

DNA↗

PubMed1996

Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci.

In order that there can be confidence that DNA profile frequency estimates will not place undue bias against a defendant, 2 methods are described for estimating minimum allele frequency bounds for PCR-based loci. One approach estimates minimum allele frequencies for VNTR and STR loci using sample size and the observed heterozygosity at a locus, while the second approach, appropriate for loci typed with allele-specific oligonucleotide probes, is based only on sample size. The use of a minimum allele frequency enables compensation for sparse sampling of infrequent alleles in population databases.

DNA Fingerprinting↗

PubMed1996

Determination of cadmium by electrothermal atomic absorption spectrometry after microwave-assisted digestion of animal tissues and sewage sludges.

The determination of cadmium in different sample types has been carried out by electrothermal atomization atomic absorption spectrometry with D(2)-background correction using a unpyrocoated graphite tube, after pressurized microwave-assisted digestion. Five chemical modifiers [(NH(4))(2)HPO(4), Pd(NO)(3))(2), Ni(NO(3))(2), thiourea and Triton X-100] have been assayed and nickel nitrate has been found to be most effective for an accurate determination of cadmium in mussel tissue, pig kidney and sewage sludge. The characteristic mass of the method is of the order of 1 pg and the limit of detection is lower than 0.1 ng/ml.

Journal Article↗

PubMed1996

Literature study of microwave-assisted digestion using electrothermal atomic absorption spectrometry.

The literature on the use of microwave-assisted digestion procedures for subsequent sample analysis by means of electrothermal atomic absorption spectrometry (ETAAS) is reviewed. The literature survey reveals that this digestion technique has been applied mainly for biological materials. The elements most extensively determined by this method are cadmium and lead followed by copper, chromium, nickel and iron. The microwave digestion conditions, ETAAS furnace programmes and analytical details of the developed methodologies have been carefully revised.

Journal Article↗

PubMed1996

A genome-wide search for human non-insulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2.

Non-insulin-dependent (type 2) diabetes mellitus (NIDDM) is a common disorder of middle-aged individuals characterized by high blood glucose levels which, if untreated, can cause serious medical complications and lead to early death. Genetic factors play an important role in determining susceptibility to this disorder. However, the number of genes involved, their chromosomal location and the magnitude of their effect on NIDDM susceptibility are unknown. We have screened the human genome for susceptibility genes for NIDDM using non-and quasi-parametric linkage analysis methods in a group of Mexican American affected sib pairs. One marker, D2S125, showed significant evidence of linkage to NIDDM and appears to be a major factor affecting the development of diabetes mellitus in Mexican Americans. We propose that this locus be designated NIDDM1.

Chromosomes, Human, Pair 2↗

PubMed1996

Dynamics of repeat polymorphisms under a forward-backward mutation model: within- and between-population variability at microsatellite loci.

Suggested molecular mechanisms for the generation of new tandem repeats of simple sequences indicate that the microsatellite loci evolve via some of forward-backward mutation. We provide a mathematical basis for suggesting a measure of genetic distance between populations based on microsatellite variation. Our results indicate that such a genetic distance measure can remain proportional to the divergence time of populations even when the forward-backward mutations produce variable and/or directionally biased alleles size changes. If the population size and the rate of mutation remain constant, then the measure will be proportional to the time of divergence of populations. This genetic distance is expressed in terms of a ratio of components of variance of allele sizes, based on expressions developed for studying population dynamics of quantitative traits. Application of this measure to data on 18 microsatellite loci in the nine human populations leads to evolutionary trees consistent with the known ethnohistory of the populations.

Alleles↗

PubMed1996

Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations.

We have analyzed five microsatellite loci from the nonrecombining portion of the human Y chromosome in 15 diverse human populations to evaluate their usefulness in the reconstruction of human evolution and early male migrations. The results show that, in general, most populations have the same set of the most frequent alleles at these loci. Hypothetical ancestral haplotypes, reconstructed on the basis of these alleles and their close derivatives, are shared by multiple populations across racial and geographical boundaries. A network of the observed haplotypes is characterized by a lack of clustering of geographically proximal populations. In spite of this, few distinct clusters of closely related populations emerged in the network, which are associated with population-specific alleles. A tree based on allele frequencies also shows similar results. Lack of haplotypic structure associated with the presumed ancestral haplotypes consisting of individuals from almost all populations indicate a recent common ancestry and/or extensive male migration during human evolutionary history. The convergent nature of microsatellite mutation confounds population relationships. Optimum resolution of Y chromosome evolution will require the use of additional microsatellite loci and diallelic genetic markers with lower mutation rates.

Alleles↗

PubMed1996

Distribution and evolution of CTG repeats at the myotonin protein kinase gene in human populations.

We have analyzed the CTG repeat length and the neighboring Alu insertion/deletion (+/-) polymorphism in DNA samples from 16 ethnically and geographically diverse human populations to understand the evolutionary dynamics of the myotonic dystrophy-associated CTG repeat. Our results show that the CTG repeat length is variable in human populations. Although the (CTG)5 repeat is the most common allele in the majority of populations, this allele is absent among Costa Ricans and New Guinea highlanders. We have detected a (CTG)4 repeat allele, the smallest CTG known allele, in an American Samoan individual. (CTG) > or = 19 alleles are the most frequent in Europeans followed by the populations of Asian origin and are absent or rare in Africans. To understand the evolution of CTG repeats, we have used haplotype data from the CTG repeat and Alu(+/-) locus. Our results are consistent with previous studies, which show that among individuals of Caucasian and Japanese origin, the association of the Alu(+) allele with CTG repeats of 5 and > or = 19 is complete, whereas the Alu(-) allele is associated with (CTG)11-16 repeats. However, these associations are not exclusive in non-Caucasian populations. Most significantly, we have detected the (CTG)5 repeat allele on an Alu(-) background in several populations including Native Africans. As no (CTG)5 repeat allele on an Alu(-) background was observed thus far, it was proposed that the Alu(-) allele arose on a (CTG)11-13 background. Our data now suggest that the most parsimonious evolutionary model is (1) (CTG)5-Alu(+) is the ancestral haplotype; (2) (CTG)5-Alu(-) arose from a (CTG)5-Alu(+) chromosome later in evolution; and (3) expansion of CTG alleles occurred from (CTG)5 alleles on both Alu(+) and Alu(-) backgrounds.

Biological Evolution↗

PubMed1996

Segregation distortion of the CTG repeats at the myotonic dystrophy locus.

Myotonic dystrophy (DM), an autosomal dominant neuromuscular disease, is caused by a CTG-repeat expansion, with affected individuals having > or = 50 repeats of this trinucleotide, at the DMPK locus of human chromosome 19q13.3. Severely affected individuals die early in life; the milder form of this disease reduces reproductive ability. Alleles in the normal range of CTG repeats are not as unstable as the (CTG)(> or = 50) alleles. In the DM families, anticipation and parental bias of allelic expansions have been noted. However, data on mechanism of maintenance of DM in populations are conflicting. We present a maximum-likelihood model for examining segregation distortion of CTG-repeat alleles in normal families. Analyzing 726 meiotic events in 95 nuclear families from the CEPH panel pedigrees, we find evidence of preferential transmission of larger alleles (of size < or = 29 repeats) from females (the probability of transmission of larger alleles is .565 +/- 0.03, different from .5 at P approximately equal .028). There is no evidence of segregation distortion during male meiosis. We propose a hypothesis that preferential transmission of larger CTG-repeat alleles during female meiosis can compensate for mutational contraction of repeats within the normal allelic size range, and reduced viability and fertility of affected individuals. Thus, the pool of premutant alleles at the DM locus can be maintained in populations, which can subsequently mutate to the full mutation status to give rise to DM.

Alleles↗

PubMed1996

Paternity exclusion by DNA markers: effects of paternal mutations.

In parentage testing when one parent is excluded, the distribution of the number of loci showing exclusion due to mutations of the transmitting alleles is derived, and it is contrasted with the expected distribution when the exclusion is caused by nonpaternity. This theory is applied to allele frequency data on short tandem repeat loci scored by PCR analysis, and VNTR data scored by Southern blot RFLP analysis that are commonly used in paternity analysis. For such hypervariable loci, wrongly accused males should generally be excluded based two or more loci, while a true father is unlikely to be excluded based on multiple loci due to mutations of paternal alleles. Thus, when these DNA markers are used for parentage analysis, the decision to infer non-paternity based on exclusions at two or more loci has a statistical support. Our approach places a reduced weight on the combined exclusion probability. Even with this reduced power of exclusion, the probability of exclusion based on combined tests on STR and VNTR loci is sufficiently large to resolve most paternity dispute cases in general populations.

Adult↗

PubMed1996

Immunoglobulin allotypes and estimation of genetic admixture among populations of Kinnaur District, Himachal Pradesh, India.

Four regional populations of the Kanet (Puh, Kalpa, Sangla, and Nachar) and an endogamous group of Koli from Kinnaur District, Himachal Pradesh, India, were studied to determine the extent of genetic variation of immunoglobulin allotypes (GM, KM, and AM) and the genetic contribution from ancestral populations of Tibet and northwest India. Haplotype GM*A G showed a higher frequency in the Kanet (40-60%)-a frequency that is more comparable to Asian populations-whereas in the Koli a lower frequency was observed, which is nearer the values for populations from northwest India. The IG haplotype data suggest that the Kanet population of Kinnaur District and the northeastern population of Nepal have different European origins than the more central population of India, represented by a sample from Delhi. The present results suggest that the populations of Kinnaur District are of admixed origin with contributions of Tibetan genes of 87.3%, 51.3%, 49.9%, 40.0%, and 9.5% in the Puh, Kalpa, Sangla, and Nachar Kanet and the Koli, respectively. The genetic distance obtained from 19 loci (9 blood groups, 8 biochemical markers, GM, and KM) showed an inverse relationship between the distance of the hybrid population from the parental gene pool. The Puh Kanet, nearest the Tibetan border, had the highest proportion of Tibetan genes but showed the lowest genetic distance with Tibetans. As the geographic distance of the other regional populations of the Kanet increases from the border of Tibet, genetic distance compared with the parental Tibetan population increases and the proportion of Tibetan admixture decreases. In the Kinnaur District admixture seems to contribute largely to the present-day observed high level of genetic differentiation.

Ethnicity↗

PubMed1996

Population genetic study of three VNTR loci (D2S44, D7S22, and D12S11) in five ethnically defined populations of the Indian subcontinent.

Using RFLP (restriction fragment length polymorphism) analysis, we have characterized the genotypic variation of three VNTR (variable number of tandem repeat) loci (D2S44, D7S22, and D12S11) with probes YNH24, g3, and MS43a, respectively, for 288 individuals from 5 genetically well-defined ethnic groups (Brahmins, Maratha, Gujarati Patel, Sinhalese, and Moors) of the Indian subcontinent. The distributions of VNTR alleles at the binned level were examined among the five populations, and the genetic affinities obtained using the VNTR data were compared with serogenetic data on 22 blood group and protein loci previously reported from our laboratory. For classical genetic markers the Sinhalese show slight affinity with the populations of western India. However, the genetic affinity results considerably parallel the results for VNTR loci and 25 combined VNTR/blood group/protein loci, suggesting that the Sinhalese show the least affinity with the populations of western India. These results confirm the findings of a recent study of genetic relationships of the populations of Sri Lanka based on admixture analysis. The concerns regarding whether or not the pattern of genetic variation of VNTR loci at the bin level can be studied using classical population principles are addressed.

Ethnicity↗

PubMed1995

Intra- and inter-population diversity at short tandem repeat loci in diverse populations of the world.

To study the level of intra- and inter-population variation at hypervariable DNA loci, we have characterized 15 human populations of diverse ethnic and geographic origins at six short tandem repeat loci by using the polymerase chain reaction. Even though the spectrum of allelic variation is quite broad and there are substantial differences in allele frequency distributions among populations, in general, population within a major racial group show a greater degree of similarity. This observation is reflected in the analysis of gene diversity. When the total diversity is apportioned, the maximum variation becomes attributable to inter-individual differences within a population; of the variation that is attributed to differences between populations within a racial group and differences between racial groups, namely, African, Caucasian, and Mongoloid, than the American Indians and the Pacific Islanders. As expected, a reciprocal relationship between gene diversity and FST levels is observed. Higher values of FST in the American Indian and the Pacific Islanders may reflect smaller population size and a higher level of isolation. An analysis of genetic distance encompassing the populations belonging to the three major racial groups recognizes three distinct clusters - all the populations of African affiliation cluster together, as do the Caucasian affiliated and the Mongoloid groups, in two distinct clusters. Interestingly, three broadly classified cosmopolitan US populations, namely, US White, US Black and US Asian, cluster with their ancestrally related populations. This study dispels some of the concerns regarding the applicability of DNA typing data for forensic use.

Alleles↗

PubMed1995

Phylogeny of six Sciurus aberti subspecies based on nucleotide sequences of cytochrome b.

The tassel-eared squirrel, Sciurus aberti, is separated into six subspecies which occupy restricted and comparable habitats in ponderosa pine forests in the south-western United States and Mexico. These forests and squirrel populations are currently isolated by large arid areas and, as such, S. aberti appears to offer an example of incipient speciation. We sequenced the complete mitochondrial cytochrome b gene to construct a molecular phylogeny for S. aberti and to determine whether subspecific genetic structure and geographic patterns are correlative. Twenty alleles were identified among 612 squirrels throughout the species' range. Nucleotide divergence between alleles ranged from 0.009 to 0.0233, whereas average sequence divergence between S. aberti and an outgroup species, Sciurus niger, was 0.1823. Neighbor-joining and maximum parsimony analyses identified three major genetic assemblages composed of the following subspecies groups: (1) barberi and durangi; (2) aberti and kaibabensis; and (3) ferreus. The chuscensis samples were the only population with divergent sequences; one sequence was identical to an aberti sequence and a second unique sequence clustered with the ferreus sequences. The presence of divergent sequences in the chuscensis population, coupled with its central geographic position between aberti and ferreus, suggests a relatively recent influx of aberti mtDNA. Estimates of the times separating sequences in subspecies within different groups ranged from 0.94 to 1.52 x 10(6) years, based on a rate estimate of 7.15 x 10(-9) substitutions/year/site. The limited divergence observed between (1) aberti and kaibabensis as well as (2) barberi and durangi suggests relatively recent separations of subspecies within each assemblage. In fact, populations defined morphologically and geographically as ferreus exhibited greater sequence divergence than the aforementioned groups, identifying ferreus as the subspecies with the greatest genetic substructuring. The levels of cytochrome b divergence observed for the three distinct groups argues against a significant role for late Pleistocene glaciation in dispersal of this particular species; however, the proposed intermixing of aberti and chuscensis populations may well have been associated with such glacial events. Nucleotide diversity within subspecies ranked chuscensis >> aberti > barberi approximately kaibabensis approximately ferreus subpopulations; the relatively high level of diversity of chuscensis samples likely results from the apparent introgression of an aberti haplotype. The comparative levels of diversity in the aberti, barberi, kaibabensis, and ferreus sample populations do not correlate with respective habitat size (and presumably population size), suggesting that relatively recent forces, e.g., glaciation and inconsistent timber harvests, may have influenced diversity in these populations without apparent alterations in population size.

Amino Acid Sequence↗

PubMed1995

Correlation of DNA fragment sizes within loci in the presence of non-detectable alleles.

At present most forensic databases of DNA profiling of individuals consist of DNA fragment sizes measured from Southern blot restriction fragment length polymorphism (RFLP) analysis. Statistical studies of these databases have revealed that, when fragment sizes are measured from RFLP analysis, some of the single-band patterns of individuals may actually be due to heterozygosity of alleles in which fragment size resulting from one allele remains undetected. In this work, we evaluate the effect of such allelic non-detectability on correlation of fragment sizes within individuals at a locus, and its impact on the inference of independence of fragment sizes within loci. We show that when non-detectable alleles are present in a population at a locus, positive correlations of fragment sizes are expected, which increase with the proportion of non-detectable alleles at the locus. Therefore, a non-zero positive correlation is not a proof of allelic dependence within individuals. Applications of this theory to the current forensic RFLP databases within the US show that there is virtually no evidence of significant allelic dependence within any of the loci. Therefore, the assumption that DNA fragment sizes within loci are independent is valid, and hence, the population genetic principles of computing DNA profile frequencies by multiplying binned frequencies of fragment sizes are most likely to be appropriate for forensic applications of DNA typing data.

Alleles↗

PubMed1995

Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics.

In a substructured population the overall heterozygote deficiency can be predicted from the number of subpopulations (s), their time of divergence (t), and the nature of the mutations. At present the true mutational mechanisms at the hypervariable DNA loci are not known. However, the two existing mutation models (the infinite allele model (IAM) and the stepwise mutation model (SMM)) provide some guides to predictions from which the possible effect of population substructuring may be evaluated, assuming that the subpopulations do not exchange any genes among them during evolution. The theory predicts that the loci with larger mutation rate, and consequently showing greater heterozygosity within subpopulations, should exhibit a smaller proportional heterozygote deficiency (GST) and, hence, the effects of population substructuring should be minimal at the hypervariable DNA loci (an order of magnitude smaller than that at the blood group and protein loci). Applications of this theory to data on six Variable Number of Tandem Repeat (VNTR) loci and five short tandem repeat (STR) loci in the major cosmopolitan populations of the USA show that while the VNTR loci often exhibit a large significant heterozygote deficiency, the STR loci do not show a similar tendency. This discordant finding may be ascribed to the limitations, coalescence and nondetectability of alleles associated with the restriction fragment length polymorphism (RFLP) analysis through which the VNTR loci are scored. Such limitations do not apply to the polymerase chain reaction (PCR) method, through which the STR loci are scored. The implications of these results are discussed in the context of the forensic use of DNA typing data.

DNA↗

PubMed1995

A novel measure of genetic distance for highly polymorphic tandem repeat loci.

Genetic distance measures are indicators of relatedness among populations or species and are useful for reconstructing the historic and phylogenetic relationships among such groups. Classical measures of genetic distance were developed to analyze biochemical and serological polymorphisms, systems which generally show limited variability. However, these traditional measures of genetic distance are inadequate for the analysis of certain classes of variable number tandem repeat (VNTR) loci, which have a larger number of alleles and higher levels of heterozygosity than traditional genetic markers. At the higher levels of heterozygosity observed at these loci, the standard measures of genetic distance are nonlinear and do not account for the mutational mechanisms of hypervariable loci. We have developed a measure of genetic distance, DSW, which is appropriate for the analysis of highly polymorphic DNA loci. Using computer simulations of diverging populations, we show that DSW conforms to linearity and that the variance is similar in magnitude to traditional measures of genetic distance. Comparisons of phylogenetic trees derived from the simulated divergence of human racial groups demonstrate that the branch lengths of trees prepared using DSW are more similar to the model tree than those generated using other measures. Finally, we demonstrate the applicability of DSW to evolutionary analysis by reconstructing the relationships among eight human populations using 14 microsatellite and STR loci. The phylogenetic trees generated using DSW are different from trees constructed with traditional measures and better reflect the well-documented ancient divergence of African and non-African populations.

Animals↗

PubMed1995

Cancer predisposition, radiosensitivity and the risk of radiation-induced cancers. I. Background.

This paper presents an overview of current knowledge on genetic predisposition to cancer and on enhanced sensitivity of cancer-predisposed genotypes to cancers induced by ionizing radiation. It is intended to provide a background and set the stage for the next papers in this series in which we will assess how such heterogeneity (with respect to predisposition to cancer and presence of radiosensitivity genotypes) in a population may affect estimates of the risk of radiation-induced cancers. The main findings and/or conclusions of the present paper are the following: (1) "Cancer-predisposing genes" (i.e. those at which germinal mutations predispose to cancer) are present in the human genome; these genes are responsible not only for the rare familial cancer syndromes but also for a proportion of the common cancers. At least 21 such genes have now been cloned (including 9 tumor suppressor genes, 11 DNA repair genes and 1 proto-oncogene); further, at least 8 putative tumor suppressor genes and a gene involved in ataxia telangiectasia have been localized to specific chromosomes. (2) These genes play crucial roles in the control of cellular proliferation, programmed cell death (apoptosis) and/or one or another DNA repair pathway. Consequently, mutations in these genes are likely to "liberate" the cells from the normal constraints imposed by them, resulting in unconstrained growth characteristic of cancer. (3) At present, the evidence for increased sensitivity of cancer-predisposed genotypes to radiation-induced cancers is limited. However, current knowledge of the known functions of the cancer-predisposing genes and of the consequences of mutations in these provide (a) sufficient grounds for assuming that the genotypes of those predisposed to cancer may be at an increased risk for radiation-induced cancers and (b) the rationale for attempts to estimate quantitatively the impact of genotype-dependent differences in cancer predisposition and radiosensitivity on cancer risks in an irradiated population.

Animals↗