Complex segregation analysis of facial clefting in Chile

Nonsyndromic cleft lip with or without cleft palate (CL/P) has an incidence of 1.5 per 1,000 live births in Chile, with 1.7 per 1,000 in males and 1.3 per 1,000 in females, which is nearly the same as the level found in Asian populations. The high rate of occurrence of CL/P in Chile is probably due to the presence of Amerindian genes in Chilean populations. Using the computer program PAP, a complex segregation analysis of CL/P was conducted for 67 multigeneration pedigrees from Chile, each ascertained from one affected proband. These pedigrees yielded 162 affected individuals and over 898 family members who were included in the analysis. The most parsimonious model of transmission indicated the presence of an autosomal dominant gene with reduced (20-25%) penetrance.

Historical genetics in Uruguay: estimates of biological origins and their problems

The relative contribution of Europeans, Africans, and Amerindians to the gene pool of two Uruguayan populations (Montevideo and Tacuarembó) was estimated using several approaches. For Montevideo 8 genetic systems were considered, and for Tacuarembó 18 systems were used. A preliminary investigation of the most probable parental groups, using genetic distances, yielded four combinations of European populations, four combinations of African populations, and five combinations of Amerindian populations. Afterward, 240 possible combinations from the possible parental groups were considered for the quantitative estimations of interethnic admixture using the gene identity method. The most inclusive combinations furnished the following admixture estimates: (1) Montevideo, 92% European, 7% African, and 1% Amerindian; (2) Tacuarembó, 65% European, 15% African, and 20% Amerindian. The modal values obtained within each ethnic category did not differ by much (2-3%), the exception being the Amerindian contribution to Tacuarembó, where a higher diversity was observed (up to 14%). Comparison with a maximum-likelihood method of admixture estimation was hampered by the fact that not all markers can be used to obtain these alternative numbers. Evaluations using six systems for Montevideo and seven for Tacuarembó yielded values that were closer to the previous estimates for Montevideo (largest difference, 7% in the Amerindian component) but somewhat higher for Tacuarembó, amounting to 11% for the European and Amerindian contributions. It is clear, however, that the two populations show significant biological heterogeneity, resulting partly from diverse patterns of historical formation.

A test of allelic independence based on distributions of allele size differences at microsatellite loci

Thousands of polymorphic microsatellite loci are now mapped in the human genome, most of which exhibit a large number of segregating alleles. For forensic, evolutionary and gene mapping applications, it is important to establish intralocus allelic independence at these loci. We develop a test for intralocus allelic independence based on repeat size differences between alleles within genotypes of individuals, and show its relationship with the intraclass correlation of allele sizes within loci. Applications of this test to 13 short tandem repeat loci in 4 subpopulations indicate that the distribution of size differences of alleles has adequate power to detect intralocus dependence of alleles caused by population substructure. In addition, size differences between randomly chosen alleles provide information regarding heterozygosity and contiguity of allele sizes at the locus, which by themselves do not necessarily indicate the presence of population substructure.

Cancer predisposition, radiosensitivity and the risk of radiation-induced cancers. III. Effects of incomplete penetrance and dose-dependent radiosensitivity on cancer risks in populations

Recent studies have identified a number of genes in the human genome at which germinal mutations predispose the individuals to one or another type of cancer. These studies also show that not all individuals carrying the mutant genes develop cancers (i.e., the mutant genes are not fully penetrant). At least some of these predisposed genotypes also have a higher sensitivity to cancers induced by ionizing radiation than those who are not so predisposed, which may be dependent on dose. This paper presents an analysis of the impact of such heterogeneity on estimates of cancer risks for an irradiated population. This is done by extending the Mendelian one-locus, two-allele model of cancer predisposition and radiosensitivity developed earlier to allow for incomplete penetrance and dose dependence of radiosensitivity differentials among genotypes. The model is applied to recently published data for breast cancer and hereditary non-polyposis colon cancer using a range of possible values for the strength of predisposition and radiosensitivity differentials. It is shown that, after radiation exposures, the ratio of cancer risks in a heterogeneous population relative to that in a homogeneous population increases with increasing dose, but that the dose dependence of the relative risk diminishes at higher doses. Likewise, the attributable risk (i.e. the proportion of the increase in risk that is due to both increased susceptibility and increased radiosensitivity) and the proportion of attributable risk due to increased radiosensitivity also increase with dose, and the dose dependence of each measurement also diminishes at higher doses. However, when the proportion of cancers due to the susceptible genotypes is small (<10%) (as is likely to be the case for breast cancer in non-Ashkenazi women), the increases in the relative risk and attributable risk are marked only when there are very large increases in cancer susceptibility (>1000-fold) and radiosensitivity (>100-fold) in the susceptible group. When the proportion of cancers due to the susceptible genotypes is appreciable (> or = 10%) (as may be the case for breast cancer in Ashkenazi Jewish women), there may be large increases in the relative risk and attributable risk for comparatively modest increases in cancer susceptibility (>10-fold) and radiosensitivity (>100-fold) in the susceptible subpopulation. For any given combination of strength of predisposition and radiosensitivity differential, incomplete penetrance dilutes the effect.

Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci

Using the generalized stepwise mutation model, we propose a method of estimating the relative mutation rates of microsatellite loci, grouped by the repeat motif. Applying ANOVA to the distributions of the allele sizes at microsatellite loci from a set of populations, grouped by repeat motif types, we estimated the effect of population size differences and mutation rate differences among loci. This provides an estimate of motif-type-specific mutation rates up to a multiplicative constant. Applications to four different sets of di-, tri-, and tetranucleotide loci from a number of human populations reveal that, on average, the non-disease-causing microsatellite loci have mutation rates inversely related to their motif sizes. The dinucleotides appear to have mutation rates 1.5-2 times higher than the tetranucleotides, and the non-disease-causing trinucleotides have mutation rates intermediate between the di- and tetranucleotides. In contrast, the disease-causing trinucleotides have mutation rates 3.9-6.9 times larger than the tetranucleotides. Comparison of these estimates with the direct observations of mutation rates at microsatellites indicates that the earlier suggestion of higher mutation rates of tetranucleotides in comparison with the dinucleotides may stem from a nonrandom sampling of tetranucleotide loci in direct mutation assays.

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.

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.

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.

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.

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.

Estimation of mutation rates from parentage exclusion data: applications to STR and VNTR loci

Nonpaternity is a common source of bias in estimating mutation rates when they are obtained from family data showing discordance of parental and children's genotypes. With the availability of hypervariable DNA markers, this source of bias can be largely eliminated. However, the proportion of cases where parentage exclusion is caused by presumed mutation(s) of parental alleles must be adjusted to obtain a valid mutation rate estimate. The present work derives the basis of this adjustment factor, called the proportional bias. This proportional bias depends upon the allele frequency distribution at the locus. The maximum and minimum bounds of the proportional bias depend on the number of alleles at the locus. Using data from Caucasian populations at tandem repeat loci commonly used for parentage testing and forensic identification purposes, we show that when mutation rates are estimated at these loci, the proportional bias is generally very close to the maximum possible value for the observed number of alleles (or binned fragment sizes) at each locus. The expected proportional bias decreases with increasing mutation rate at a locus. For the short tandem repeat loci, without bias correction, the direct count method can result in an underestimation of up to 60% of their true value. In contrast, for the minisatellite VNTR loci, even with crude measurements on allele sizes, we show that the absolute proportional bias is generally below the coefficient of variation of the direct estimates.

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.

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.

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.

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.

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.

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.

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.

Oxygen-dependent leishmanicidal activity of stimulated macrophages

Peritoneal macrophages pretreated with different stimulants were analysed and compared with their respective controls for their ability to kill intracellular pathogenic L. donovani, (MHOM/IN/1983/AG83) an isolate from Indian subcontinent. Stimulation of macrophages by zymosan showed a higher microbicidal activity as compared to that by PMA. A correlation between microbicidal activity of the macrophages and the parameters related to respiratory burst activity such as liberation of O2-, production of H2O2 and consumption of O2 was sought. All the parameters showed a decrease in case of infected macrophages in comparison to those of the non-infected ones. Thus, it is possible that the impairment of macrophage activation by intracellular Leishmania contributes to their survival in the toxic environment of the host.

A comparative study of genetic variation at five VNTR loci in three ethnic groups of Houston, Texas

Following the technique of Southern blot restriction fragment length polymorphisms (RFLP) analysis, we generated a database of DNA profiles at five Variable Number of Tandem Repeats loci (D1S7, D2S44, D4S139, D10S28, and D17S79) for 669 individuals of three major ethnic populations (Caucasians, Blacks, and Hispanics) of Houston, Texas. Analysis of fragment sizes at these loci within each sample, as well as their fixed-bin analyses, reveal that the assumptions of independence of allelic occurrences within and between loci are valid for this database. Fixed-bin allele frequency tables, therefore, are the best descriptors of this database for conservative forensic calculations. Finally, we demonstrate that this regional database from Houston, Texas, does not yield any meaningfully different forensic inference than the one obtained from the National database of the respective ethnic groups.

Cancer predisposition, radiosensitivity and the risk of radiation-induced cancers. II. A Mendelian single-locus model of cancer predisposition and radiosensitivity for predicting cancer risks in populations

Individuals genetically predisposed to cancer may be more sensitive to cancers induced by ionizing radiation than those who are not so predisposed. Should this be true, under conditions of radiation exposure, a population consisting of cancer-predisposed and non-predisposed individuals will be expected to respond with a higher total frequency of induced cancers than one in which all the individuals are assumed to have the same sensitivity to radiation-induced cancers. To study this problem quantitatively, we have developed a Mendelian autosomal one-locus, two-allele model; this model assumes that one of the alleles is mutant and the genotypes carrying the mutant allele(s) are cancer-predisposed and are also more sensitive to radiation-induced cancer. Formal analytical predictions as well as numerical illustrations of this model show that: (1) when such heterogeneity with respect to cancer predisposition and radiosensitivity is present in the population, irradiation results in a greater increase in the frequency of induced cancers than when it is absent; (2) this increase is detectable only when the proportion of cancers due to genetic predisposition is large and when the degree of predisposition is considerable; and (3) even when the effect is small, most of the radiation-induced cancers will occur in predisposed individuals. These conclusions are valid for models of cancer when predisposition and radiosensitivity may be either dominant or recessive. The published data on breast cancers in Japanese A-bomb survivors show that at 1 Sv, the radiation-related excess relative risk in women irradiated before age 20 is 13 compared to about 2 for those irradiated at later ages. We examined the application of our model to the above data using two assumptions, namely, that the proportion of cancers due to genetic susceptibility at the BRCA1 locus (1/200) and the frequency of the mutant allele (0.0033) estimated for Western populations are valid for Japanese women. With our model, these results can be explained only if there are very large differences in cancer susceptibility (> 1000-fold) and radiosensitivity (> 100-fold) of the heterozygotes.