Polymorphisms of p53 codon 72 and MDM2 promoter 309 and the risk of endometrial cancer

Genetic polymorphisms of p53 and its negative regulator murine double minute 2 homolog (MDM2) have been shown to be closely associated with tumorigenesis in a variety of human cancers. In the present study, single nucleotide polymorphism (SNP) at p53 codon 72 and MDM2 promoter 309 was examined for germline DNA samples from 102 endometrial cancer cases and 95 controls using polymerase chain reaction-based fragment analysis. There were no significant differences in the genotype and allele prevalence between control subjects and endometrial cancer patients for p53 codon 72. The GG genotype frequency of MDM2-SNP309 was statistically higher in endometrial cancer patients than that in normal healthy women when compared with the TG genotype ( P = 0.0088). However, no statistically significant differences were found between the TT and TG or GG genotype frequencies and allele prevalence. Interestingly, the combination of the homozygous Arg/Arg genotype of p53 codon 72 and homozygous GG genotype of MDM2 SNP309 polymorphisms was significantly associated with the risk of endometrial cancer (odds ratio = 3.28, 95% confidence interval = 1.13 to 9.53, P = 0.0212). The homozygous variants of wild p53 codon 72 and mutant MDM2 promoter 309 may cooperatively increase the risk of endometrial cancer in a Japanese population.     

Evidence for familial factors that protect against dementia and outweigh the effect of increasing age.

A positive family history is associated with increased risk for dementia. It is not known whether a negative family history with long-lived relatives predicts a reduced risk for dementia. We studied the survival rate and the occurrence of dementia in 232 parents and siblings of 43 optimally healthy individuals > or = 84 years of age and compared them with 233 parents and siblings of 51 random controls and 499 parents and siblings of 88 Alzheimer disease (AD) patients. Prevalence of dementia after age 60 years was .031 for the relatives of healthy elderly, .066 for the relatives of random controls, and .217 for the relatives of AD patients. The cumulative incidence of dementia by age 85 years was estimated as .041 (+/- .019) for the relatives of healthy elderly individuals, .102 (+/- .038) for the relatives of random controls, and .360 (+/- .037) for the relatives of AD patients. Hazard-ratio estimates suggest that the risk of dementia for the relatives of healthy elderly is 3 times lower than the risk for the relatives of random controls (P < .03) and is 11 times lower than the risk for the relatives of AD patients (P < .00005). An analysis of age at death indicated that the relatives of healthy elderly and the relatives of AD patients had a longer life span than did the relatives of random controls.(ABSTRACT TRUNCATED AT 250 WORDS)     

Genetic-epidemiologic study of adenoma and cancer of the large intestine]

A clinical/genealogical study of colorectal adenomas (CRA) and cancer (CRC), and multiple primary malignant tumors (MPMT) was performed. The CRA prevalence in the population was 4.7 +/- 1.4% (single CRA--6.3% and multiple CRA--3.0%). The frequencies of malignant adenomas, 0.7% CRC, and MPMT were 0.7, 0.17 +/- 0.07%, and 0.004 +/- 0.003%, respectively. The prevalence of cancer of the female reproductive organs was also estimated (cancer of uterine body, 0.2 +/- 0.1%; cancer of ovaries, 0.08 +/- 0.1%; cancer of uterine cervix, 0.55 +/- 0.1%; cancer of mammary gland 0.57 +/- 0.1%). The main parameters of the familial inheritance of adenomas, CRC, and MPMT were also studied in general and at various clinical variants of these pathologies. Among the first-degree relatives of patients with solitary and multiple adenomas, the adenoma frequencies were 5.9 +/- 0.6 and 3.7 +/- 0.5%, respectively. The CRC frequency among the first-degree relatives of patients with adenoma was 3.0 +/- 0.6% and the frequency of MPMT was 5.8 +/- 0.6%. On the basis of the data obtained on frequencies of malignant tumors in various groups of relatives, the following conclusions were made: (1) in families of each proband group, specific pathology was accumulated; (2) the familial frequency of malignant tumors increased with an increase in proliferative processes and the severity of a pathology in probands.     

CDKN2A mutations and MC1R variants in Italian patients with single or multiple primary melanoma

We evaluated the contribution of germline CDKN2A mutations and MC1R variants to the development of melanoma in a hospital-based study of single (SPM, n = 398) and multiple primary melanoma (MPM, n = 95). The overall frequency of CDKN2A mutations was 15.2%, and four-fold higher in MPM than in SPM cases (OR = 4.27; 95% CI 2.43-7.53). The likelihood of identifying a CDKN2A mutation increased with family history of melanoma and younger age at diagnosis in MPM cases. Compared to SPM patients, the risk of harboring a CDKN2A mutation rose as the number of primary melanomas increased and was not influenced by family history. The G101W and E27X founder mutations were the most common. Several other mutations (W15X, Q50X, R58X, A68L, A127P and H142R) were detected for the first time in Italian patients. One novel mutation, T77A, was identified. Several non-coding variants with unknown functional significance were also found (5'UTR -25C > T, -21C > T, -67G > C, IVS1 +37G > C); the novel 5'UTR -21C > T variant was not detected in controls. The CDKN2A A148T polymorphism was more frequent in MPM patients than in the control population (15.7% versus 6.6%). Compared to the SPM patients, MPM cases had a 2-fold increased probability of being MC1R variant carriers and a higher probability of carrying two or more variants. No specific association was observed between the type of variant and the number of melanomas, suggesting that the number rather than the type of MC1R variant increases the risk of MPM. We observed no interaction between CDKN2A status and the presence of MC1R variants. The high frequency of CDKN2A mutations in our MPM cases, independent of their family history, is of relevance to genetic counseling and testing in our population.     

Identification of insulin receptor systems: assessing the impact of model selection and measurement error on precision of parameter estimates using Monte Carlo study

An extensive Monte Carlo study has been carried out in order to study the effect of measurement error on the precision of parameter estimates of an insulin binding system. Hypothetical radioimmunoassay experiments were generated for insulin binding to erythrocytes. The design of experiments followed strictly the protocol of real experiments. Randomly generated error was added to the synthetic data. The standard technique, a weighted non-linear regression analysis, was employed to re-estimate parameters of a model of two receptor sites and a model of negative co-operativity. As the original parameter values were known, the differences between original and estimated values was studied for (a) measurement error in the range from 0-17%, (b) random initial estimates and (c) error-free non-specific binding. In addition, analytical estimates of parameter precision were compared with the true between-experiment variation of parameter estimates. At the measurement error of 12%, a one site model is recommended to estimate the high affinity population of the two sites model. Plausible results can be expected in 90% of experiments, the between-experiment variation being approximately 30%. The model of two receptor sites gives approximately two thirds of plausible results. The high affinity population can be estimated with the between-experiment variation of 40%, the low affinity population is virtually unidentifiable with the between-experiment variation of approximately 100% and parameter estimates biased to higher values. Only half of the results obtained from the model of negative co-operativity are plausible, the variation in parameter estimates ranges from 90-150% and estimates are biased to higher values. At the level of 12% measurement error, random initial estimates do not significantly affect the estimation process, provided initial estimates are selected from a feasible range. At the same measurement error, the error-free non-specific binding does not improve the results, indicating that the mean of six replicates may be taken as a reliable estimate of non-specific binding. The analytical estimates of the coefficient of variation systematically underestimates the true between-experiments coefficient of variation, the difference has been found to be about 50%.     

Genetic analysis of the structure of the predisposition to diabetes mellitus. II. The prevalence, morbidity and heritability of diabetes mellitus

Prevalence of diabetes mellitus (D.M.) was estimated in several Moscow districts. The prevalence increases with the age from 0.073 in males and 0.085% in females at the age of 16-19 yrs to 4.9 in males and 6.2% in females at the age of 75 yrs and older. The overall prevalence of D.M. was 1.12%. The morbidity risks have the same patterns of increase: from 0.007 and 0.008% at the age of 0-4 yrs to 1.6 and 2.7% at the age of 75 yrs and older in males and females, respectively. The values of "cumulative" morbidity risk, for the population living long enough, derived from the estimates of age-specific morbidity risks were 6.57 for males and 11.93% for females. The estimate of correlation between first-degree relatives at onset-age of D.M. was 0.307. Accounted for the age-at-onset of the probands and for current ages of siblings, the estimates of recurrence risks, i.e. the probability to develop D.M. for siblings living long enough, were: 27.28 for sisters of the male-probands, 21.59 for sisters of the female-probands, 19.28 for brothers of male-probands and 9.62% for brothers of the female-probands. Thus, the family distribution of D.M., according to the sex of the probands and that of their relatives corresponds to the multifactorial model of inheritance for the diseases with sex-specific thresholds. The estimates of correlation in liability and that of heritability of D.M. calculated from the data on sibs, were 0.284 +/- 0.0351 and 0.568 +/- 0.0702, respectively. The data obtained show that hereditary factors play an essential role in the development of D.M. These results are of a practical interest for genetic counselling, as well as for establishing the preventive measures in the Public Health Service.     

A Comparison of Grizzly Bear Demographic Parameters Estimated from Non-Spatial and Spatial Open Population Capture-Recapture Models

Capture-recapture studies are frequently used to monitor the status and trends of wildlife populations. Detection histories from individual animals are used to estimate probability of detection and abundance or density. The accuracy of abundance and density estimates depends on the ability to model factors affecting detection probability. Non-spatial capture-recapture models have recently evolved into spatial capture-recapture models that directly include the effect of distances between an animal’s home range centre and trap locations on detection probability. Most studies comparing non-spatial and spatial capture-recapture biases focussed on single year models and no studies have compared the accuracy of demographic parameter estimates from open population models. We applied open population non-spatial and spatial capture-recapture models to three years of grizzly bear DNA-based data from Banff National Park and simulated data sets. The two models produced similar estimates of grizzly bear apparent survival, per capita recruitment, and population growth rates but the spatial capture-recapture models had better fit. Simulations showed that spatial capture-recapture models produced more accurate parameter estimates with better credible interval coverage than non-spatial capture-recapture models. Non-spatial capture-recapture models produced negatively biased estimates of apparent survival and positively biased estimates of per capita recruitment. The spatial capture-recapture grizzly bear population growth rates and 95% highest posterior density averaged across the three years were 0.925 (0.786–1.071) for females, 0.844 (0.703–0.975) for males, and 0.882 (0.779–0.981) for females and males combined. The non-spatial capture-recapture population growth rates were 0.894 (0.758–1.024) for females, 0.825 (0.700–0.948) for males, and 0.863 (0.771–0.957) for both sexes. The combination of low densities, low reproductive rates, and predominantly negative population growth rates suggest that Banff National Park’s population of grizzly bears requires continued conservation-oriented management actions.     

Analysis of the qualitative dermatoglyphics of the digito-palmar complex in patients with primary open angle glaucoma

The primary open-angle glaucomas are a group of diseases that have in common characteristic morphological changes at the optic nerve head and retinal nerve fiber layer, progressive retinal ganglion cells death and characteristic visual field loss. The risk for primary open angle glaucoma rises continuously with the level of the intraocular pressure. The disease advances slowly and there are no symptoms. Primary open angle glaucoma is caused by abnormal aqueous humour outflow in the trabecular meshwork in the open angle. Etiopathogenesis of primary open angle glaucoma is unclear. The increased risk of glaucoma in relatives has long been recognized. Frequency for manifestation of the disease is 10-30% in family members. The discovery of the specific gene loci responsible for the manifestation of glaucoma has helped us to understand its mechanism of origin and definitely confirmed the hereditary nature of this disease. Digito-palmar dermatoglyphs were already used to determine hereditary base of many diseases and it was the reason for investigation of their qualitative patterns in patients with glaucoma (22 males and 23 females), their immediate relatives (19 males and 23 females) in comparison to a group of phenotypically healthy population (52 males and 56 females). The results pointed a connection with the dermatoglyphic traits of the digito-palmar complex between patients with glaucoma and their immediate relatives. There is a possible discrimination of patients and their immediate relatives from phenotypically healthy population, too.     

Frequency of rare electrophoretic protein variants in normal human beings and in congenital pathology

17 blood proteins of infants with rough and multiple congenital malformations (CM), prematurely born infants and sick newborns without developmental anomalies were studied electrophoretically in polyacrylamide and starch gels (62422 locus tests). The control included blood samples of healthy newborns from ordinary maternity hospitals (60234 locus tests). The frequency of rare protein variants in all the cases was higher in sick children than in healthy ones. The frequency of rare genes (corrected for electrophoretically "silent" alleles) was 2.16 X 10(-3) in infants with CM and 0.99 X 10(-4) in the control. Examination of parents of 11 congenitally malformed infants with rare protein variants showed that at least in 5 cases such variants were absent in the parents and might be attributed to "fresh" mutations. However, only 3 variants (1 for serum albumin and 2 for red cell esterase) represented rare heterozygotes with codominant expression. This corresponds to the frequency of 0.59 X 10(-3). In the total population of newborns the proportion of infants with CM was 0.02, which means that the population mutation rate is 1.18 X 10(-5) per gene per generation. The data obtained support the conclusion about strong pressure of stabilizing selection against de novo mutations which change electrophoretic mobility of the protein molecule. The reasons for discrepancy between our data and the recent results of Neel and Mohrenweiser (1984) are discussed.     

The use of association data to identify family members at high risk for marker-linked diseases.

The study of genetic markers linked and associated with disease has provided important evidence of a genetic contribution to numerous diseases and has helped to establish their modes of inheritance. However, this information has not been fully utilized in counseling individuals at risk for these disorders. In the case of recessive, marker-linked diseases, such as idiopathic hemochromatosis linked to HLA in family studies and associated with specific HLA alleles in population surveys, the only current clinical application has been to identify siblings who share both HLA-marker haplotypes with the affected proband. They are considered to be presymptomatically affected, and more definitive invasive investigations are considered appropriate. All other relatives, including parents, offspring, and other siblings, who share only one marker with the proband, have been counseled only that their risk is equivalent to the gene frequency of the disease allele, for example, 3%-6% for hemochromatosis. We have developed a generally applicable method to utilize population association data to derive more specific and accurate risk figures for these other relatives of patients with marker-linked and associated diseases. We have applied this method to idiopathic hemochromatosis. If the offspring of a patient with hemochromatosis lacks A3, B7, and B14, the risk to that offspring for developing hemochromatosis is less than 2%. On the other hand, if they receive HLA A3 from their unaffected parent, their risk climbs to 9%-10%; if they receive an A3-B14 haplotype, their risk increases to virtually 100%. As demonstrated by our example, the application of association data to family members already at a basal increased risk for marker-linked disease can significantly refine the disease risk estimates given to those relatives. This information can be utilized to select individuals in whom invasive diagnostic testing or preventative intervention is indicated.     

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Effective population size (N_e) is a key parameter of population genetics. However, N_e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on N_e estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F_IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of N_eestimates decreased with the number of SNPs. Mean N_e estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased N_e estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.     

Analysis of common CFTR polymorphisms 5T, M470V and R75Q in healthy Serbian population

Three common CFTR polymorphisms, 5T, M470V and R75Q, have been shown to be relatively frequent in Serbian patients with monosymptomatic CF disorders. Since there is a variation in distribution of common polymorphisms among different populations, it was important to compare their frequencies in patients with the frequencies in healthy population in order to assess the possible role of these polymorphisms in the monosymptomatic CF disorders. Samples obtained from 100 healthy Serbian individuals were analyzed for the presence of CFTR 5T, M470V and R75Q variants by PSM, RFLP and DGGE methods, respectively. Allele 5T was present in two individuals, giving the allelic frequency of 1% (2/200 alleles). The frequency obtained for allele M470 was 45% (90/200 alleles), while V470 allele was present with the frequency of 55% (110/200 alleles). Polymorphism R75Q was present in two individuals, with allelic frequency of 1% (2/200 alleles). Our study has shown that the frequencies of two common polymorphisms, 5T and M470V, differ significantly in Serbian population in comparison with other South European populations. Since it appears that Serbian population has a specific distribution of studied CFTR gene variants, it would also be interesting to analyze other common variants of this gene in our population. Such data can also be potentially useful as anthropogenetic markers in population studies.     

A bootstrap assessment of variability in pedigree reconstruction based on genetic markers

The problem of assessing the variability in pedigree reconstruction using DNA markers is considered for the special case of single generation samples with no parents present. Error in pedigree reconstruction is measured through a metric imposed on the space of partitions of the individuals into family groups. A confidence set can therefore be taken to be a neighborhood of a point estimate, analogous to the estimation of a parameter in Euclidean space. The coverage probability is estimated using bootstrap techniques. Although the distributional properties of the sample depend on the population genotype frequencies, these are in practice usually unknown. Confidence sets conditioned on a statistic approximately sufficient for these frequencies are compared with confidence sets obtained by substituting frequency estimates directly into the sampling distribution. In two simulation studies, the difference is found to be of some consequence.     

Estimating the Efficacy and Efficiency of Cascade Genetic Screening

Screening for genetic variants that predispose individuals or their offspring to disease may be performed at the general population level or may instead be targeted at the relatives of previously identified carriers. The latter strategy has come to be known as "cascade genetic screening." Since the carrier risk of close relatives of known carriers is generally higher than the population risk, cascade screening is more efficient than population screening, in the sense that fewer individuals have to be genotyped per detected carrier. The efficacy of cascade screening, as measured by the overall proportion of carriers detected in a given population, is, however, lower than that of population-wide screening, and the respective inclusion rates vary according to the population frequency and mode of inheritance of the predisposing variants. For dominant mutations, we have developed equations that allow the inclusion rates of cascade screening to be calculated in an iterative fashion, depending upon screening depth and penetrance. For recessive mutations, we derived only equations for the screening of siblings and the children of patients. Owing to their mathematical complexity, it was necessary to study more extended screening strategies by simulation. Cascade screening turned out to result in low inclusion rates (<1%) when aimed at the identification of heterozygous carriers of rare recessive variants. Considerably higher rates are achievable, however, when screening is performed to detect covert homozygotes for frequent recessive mutations with reduced penetrance. This situation is exemplified by hereditary hemochromatosis, for which up to 40% of at-risk individuals may be identifiable through screening of first- to third-degree relatives of overt carriers (i.e., patients); the efficiency of this screening strategy was found to be approximately 50 times higher than that of population-wide screening. For dominant mutations, inclusion rates of cascade screening were estimated to be higher than for recessive variants. Thus, some 80% of all carriers of the factor V Leiden mutation would be detected if screening were to be targeted specifically at first- to third-degree relatives of patients with venous thrombosis. The relative cost efficiency of cascade as compared with population-wide screening (i.e., the overall savings in the extra managerial cost of the condition) is also likely to be higher for dominant than for recessive mutations. This notwithstanding, once screening has become cost-effective at the population level, it can be expected that cascade screening would only transiently represent an economically viable option.     

Estimation of the parameters of the single-locus diallele model of qualitative trait in groups of relations

The method of estimation of parameters of monolocus diallele model (MDM) of qualitative trait on relative group data is described, these parameters being the number of affected and normal proband relatives of the arbitrary family degree and siblings in different matings types. For the case of single ascertainment, the expressions of corresponding probabilities have been taken as functions of MDM parameters using ITO matrixes and genetic transition matrix. Estimation of parameters was obtained by the maximum likelyhood method. Hardy-Weinberg equilibrium is not always necessary for this method; some weak requirement of stationarity is quite enough.     

Genetico-epidemiologic analysis of the role of constitutional factors in the etiology of epilepsy

Using multifactorial and monolocus models interrelations of a number of constitutional factors of probands (sex, child convulsive reactions, character abnormalities, age at the time of illness onset) with genetic factors of epilepsy occurrence among relatives (365 families) and populations from 5 regions of the Khabarovsk krai (2.88 patients per 1000 subjects) were studied. The dependence of epilepsy manifestation probability in mutant homo- and heterozygotes on sex, convulsive reactions and age characteristics of the proband body reactivity was shown. The notions of double threshold determination of convulsive readiness (the T1 threshold "cuts" a part of population with non-paroxysmal abnormality of the brain bioelectric activity, while the T2 threshold "cuts" that with convulsive reactions) were substantiated, the presence of this causing epilepsy development in individuals with a mutant allele of the major dominant gene. The hypothesis of the ecogenetic interaction of epilepsy main etiologic factors (major gene, environmental factors and constitutional readiness) has been described.     

A Regulatory MDM4 Genetic Variant Locating in the Binding Sequence of Multiple MicroRNAs Contributes to Susceptibility of Small Cell Lung Cancer

A functional rs4245739 A>C single nucleotide polymorphism (SNP) locating in the MDM43’-untranslated (3’-UTR) region creates a miR-191-5p or miR-887-3p targeting sites. This change results in decreased expression of oncogene MDM4. Therefore, we examined the association between this SNP and small cell lung cancer (SCLC) risk as well as its regulatory function in SCLC cells. Genotypes were determined in two independent case-control sets consisted of 520SCLC cases and 1040 controls from two regions of China. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated by logistic regression. The impact of the rs4245739 SNP on miR-191-5p/miR-887-3p mediated MDM4 expression regulation was investigated using luciferase reporter gene assays. We found that the MDM4 rs4245739AC and CC genotypes were significantly associated with decreased SCLC susceptibility compared with the AA genotype in both case-control sets (Shandong set: OR = 0.53, 95% CI = 0.32–0.89, P = 0.014; Jiangsu set: OR = 0.47, 95% CI = 0.26–0.879, P = 0.017). Stratified analyses indicated that there was a significantly multiplicative interaction between rs4245739 and smoking (P _interactioin = 0.048). After co-tranfection of miRNAs and different allelic-MDM4 reporter constructs into SCLC cells, we found that the both miR-191-5p and miR-887-3p can lead to significantly decreased MDM4 expression activities in the construct with C-allelic 3’-UTR but not A-allelic 3’-UTR, suggesting a consistent genotype-phenotype correlation. Our data illuminate that the MDM4rs4245739SNP contributes to SCLC risk and support the notion that gene 3’-UTR genetic variants, impacting miRNA-binding, might modify SCLC susceptibility.     

Estimate of the penetrance of genotypes in a monolocus model taking into account environmental factors

Based on ITO matrices, a method for parameter estimation of the monolocus diallele model (MDM) of qualitative trait is described, taking account of non-genetic (environmental) factors. The model parameters, probabilities of relatives' affection, constructing the likelihood function and testing hypotheses of the effect of environmental factors on the penetrations of MDM genotypes are outlined. Examples are given, concerning estimation of epilepsy MDM parameters, taking account of two factors-harmfulness of antenatal ontogenesis period and harmfulness which provokes paroxysms.