Determining SNP allele frequencies in DNA pools

Single nucleotide polymorphisms (SNPs) are among the most common types of polymorphism used for genetic association studies. A method to allow the accurate quantitation of their allele frequencies from DNA pools would both increase throughput and decrease costs for large-scale genotyping. However, to date, most DNA pooling studies have concentrated on the use of microsatellite polymorphisms. In the case of SNPs that are restriction fragment length polymorphisms (RFLPs), studies have tended to use methods for the quantitation of allele frequency from pools that rely on densitometric evaluation of bands on an autoradiograph. Radiation-based methods have well-known drawbacks, and we present two alternative methods for the determination of SNP allele frequencies. For RFLPs, we used agarose gel electrophoresis of digested PCR products with ethidium bromide staining combined with densitometric analysis of gel images on a PC. For all types of SNP, we used allele-specific fluorescent probes in the Taqman assay to determine the relative frequencies of two different alleles. Both methods gave accurate and reproducible results, suggesting they are suitable for use in DNA pooling experiments.     

Cat gene frequencies in Richmond,California

The frequency of eight mutant genes was sampled and the results compared with studies on other cat populations for various locatities in the U.S.A.     

A recursive method for solving haplotype frequencies with application to genetics

Multiple loci analysis has become popular with the advanced developments in biological experiments. A lot of studies have been focused on the biological and the statistical properties of such multiple loci analysis. In this paper, we study one of the important computational problems: solving the probabilities of haplotype classes from a large linear system Ax = b derived from the recombination events in multiple loci analysis. Since the size of the recombination matrix A increases exponentially with respect to the number of loci, fast solvers are required to deal with a large number of loci in the analysis. By exploiting the nice structure of the matrix A, we develop an efficient recursive algorithm for solving such structured linear systems. In particular, the complexity of the proposed algorithm for the n loci problem is of O(n2(n)) operations and the memory requirement is of O(2(n)) locations for the 2(n)-by-2(n) matrix A. Numerical examples are given to demonstrate the effectiveness of our efficient solver. Finally, we apply our proposed method to analyze the haplotype classes for a set of single nucleotides polymorphisms (SNPs) from Hapmap data.     

The frequencies of constitutional chromosome abnormalities in an apparently normal adult population.

Constitutional karyotypes were determined in 1405 apparently normal adults referred for population studies of acquired chromosome abnormalities in peripheral blood lymphocytes. A total of 7 translocations (4 reciprocal, 3 Robertsonian), 1 extra structurally abnormal chromosome, 2 47,XXY and 12 inv(9) were detected. An examination of previous population studies illustrates the importance of considering differences in the resolution of the chromosome analysis when comparing frequencies of abnormalities.     

Age trends in human chiasma frequencies and recombination fractions. I. Chiasma frequencies.

Chiasma frequency data on 183 males were subjected to an analysis of covariance. There appeared to be little or no linear trend in chiasma frequency with age. This conclusion was supported by a detailed analysis of chiasma frequencies for each autosome from 21 males. There were, however, significant differences among investigators in reported mean chiasma frequencies.     

Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA

Single-nucleotide polymorphisms (SNPs) are considered useful polymorphic markers for genetic studies of polygenic traits. A new practical approach to high-throughput genotyping of SNPs in a large number of individuals is needed in association study and other studies on relationships between genes and diseases. We have developed an accurate and high-throughput method for determining the allele frequencies by pooling the DNA samples and applying a DNA microarray hybridization analysis. In this method, the combination of the microarray, DNA pooling, probe pair hybridization, and fluorescent ratio analysis solves the dual problems of parallel multiple sample analysis, and parallel multiplex SNP genotyping for association study. Multiple DNA samples are immobilized on a slide and a single hybridization is performed with a pool of allele-specific oligonucleotide probes. The results of this study show that hybridization of microarray from pooled DNA samples can accurately obtain estimates of absolute allele frequencies in a sample pool. This method can also be used to identify differences in allele frequencies in distinct populations. It is amenable to automation and is suitable for immediate utilization for high-throughput genotyping of SNP.     

Chromosome aberrations and sister-chromatid exchange frequencies in pathology staff occupationally exposed to formaldehyde

Past studies have shown that formaldehyde is mutagenic in microbial tests and Drosophila and causes chromosomal aberrations in cultured mammalian cells. Chromosomal analysis of bone marrow cells and spermatocytes from exposed laboratory animals has failed to show any genotoxic effect. Information on individuals occupationally exposed is limited and there is no evidence to date that formaldehyde can induce chromosome damage at occupational levels of exposure. This study examines the chromosome aberration and sister-chromatid exchange frequencies in lymphocytes from a group of 6 pathology workers and 5 unexposed controls. No detectable differences could be found between the groups in either chromosomal aberration induction or sister-chromatid exchange frequencies.     

Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology

Single nucleotide polymorphism (SNP) association studies searching for differences in allele frequencies between cases and controls have been widely used for genetic analysis. Individual genotyping is prohibitively expensive in large sample sizes. Pooling of samples provides the obvious advantage of higher throughput and lower cost. Here we report our results with the analysis of SNP allele frequencies in DNA pools using Pyrosequencing technology. For seven different SNPs, we observed a mean difference of 1.1 +/- 0.6% between allele frequencies determined in two different DNA pools (n = 150 cases and 150 controls) compared to individually genotyped samples.     

Geographical distribution of hot flash frequencies: considering climatic influences

Laboratory studies suggest that hot flashes are triggered by small elevations in core body temperature acting within a reduced thermoneutral zone, i.e., the temperature range in which a woman neither shivers nor sweats. In the present study, it was hypothesized that women in different populations develop climate-specific thermoneutral zones, and ultimately, population-specific frequencies of hot flashes at menopause. Correlations were predicted between hot flash frequencies and latitude, elevation, and annual temperatures. Data on hot flash frequencies were drawn from 54 studies. Pearson correlation analyses and simple linear regressions were applied, first using all studies, and second using a subset of studies that included participants only to age 60 (n = 36). Regressions were repeated with all studies, controlling for method of hot flash assessment. When analyses were restricted to studies that included women up to age 60, average temperature of the coldest month was a significant predictor of hot flash frequency (P < 0.01), explaining 29.2% of the variation in hot flash frequency. In a separate equation, the difference between hottest and coldest temperatures was also a significant predictor (P < 0.01), explaining 26.4% of the variation in hot flash frequency. When regressions used all studies but controlled for method of hot flash assessment, average temperature of the coldest month, difference between hottest and coldest temperatures, and mean annual temperature were significant predictors of hot flash frequency. Women reported fewer hot flashes in warmer temperatures, and more hot flashes with increasing seasonality. These results suggest that acclimatization to coldest temperatures or sensitivity to seasonality may explain part of the population variation in hot flash frequency.     

Analyses of gene frequencies of mates

A genic analysis of variance of data on mate pairs for a codominant gene is developed. This analysis provides estimators of the correlation, F, of genes within individuals, of the correlation, Θ, of genes between mates, and of various variances—all relative to the correlation or variation among genes of nonmates. The data are manipulated into marginal distributions to produce another method of obtaining the same estimators. Several examples are given of how assumptions about the model and parameters modify the estimators and which were utilized in constructing χ² tests of hypotheses concerning F and Θ.—A recessive gene is also considered. Only the frequency of recessive genotypes and the correlation of recessive mates are estimable in this case unless one makes very demanding assumptions about the model.—Numerical examples of the analysis of variance and estimators are given for both a codominant and recessive gene.     

Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics

Many empirical studies have revealed considerable differences between nonparametric bootstrapping and Bayesian posterior probabilities in terms of the support values for branches, despite claimed predictions about their approximate equivalence. We investigated this problem by simulating data, which were then analyzed by maximum likelihood bootstrapping and Bayesian phylogenetic analysis using identical models and reoptimization of parameter values. We show that Bayesian posterior probabilities are significantly higher than corresponding nonparametric bootstrap frequencies for true clades, but also that erroneous conclusions will be made more often. These errors are strongly accentuated when the models used for analyses are underparameterized. When data are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also conservative in this respect, but less so.     

Prediction of the frequencies of restriction endonuclease recognition sequences using di- and mononucleotide frequencies

The calculation of probabilities of nucleotide sequences from the frequencies of dinucleotides is described. The dinucleotide and mononucleotide frequencies used can be obtained from nearest neighbor analysis or from databank sequences. If dinucleotide and mononucleotide frequencies from nearest neighbor analysis are used, probabilities for oligonucleotides can be calculated for genomes in which there is little or no sequence data. Within a given genome, a broad range of probabilities for hexanucleotide palindromes with the same base composition is predicted and shown (14).     

Unusually high frequencies of HIV-specific cytotoxic T lymphocytes in humans

CTL specific for the HIV belong to the CD8 subset of T lymphocytes, and their activity is restricted by class I HLA transplantation Ag. In this report, HIV-specific CTL and their precursor cells were quantified by limiting dilution analysis. CTL were recovered from the lungs, lymph nodes, and blood of asymptomatic seropositive carriers and of patients with AIDS. HIV was found to be very immunogenic. High frequencies of both HIV-specific CTL and CTL precursor cells were detected in infected individuals. These CTL killed autologous HIV-infected macrophages and T4 lymphoblasts. They also killed doubly transfected P815-A2-env-LAV mouse tumor cells, which express the human HLA-A2 gene and the HIV-1 env gene. In the longitudinal studies of two HIV-infected patients, CTL and CTL precursor cell frequencies decreased as the clinical and immunologic status of the patients deteriorated. Most surprisingly, PBL from seronegative donors also responded to HIV stimulation in vitro and generated large numbers of HLA-restricted, HIV-specific CTL.     

HAPLOFREQ--estimating haplotype frequencies efficiently.

A commonly used tool in disease association studies is the search for discrepancies between the haplotype distribution in the case and control populations. In order to find this discrepancy, the haplotypes frequency in each of the populations is estimated from the genotypes. We present a new method HAPLOFREQ to estimate haplotype frequencies over a short genomic region given the genotypes or haplotypes with missing data or sequencing errors. Our approach incorporates a maximum likelihood model based on a simple random generative model which assumes that the genotypes are independently sampled from the population. We first show that if the phased haplotypes are given, possibly with missing data, we can estimate the frequency of the haplotypes in the population by finding the global optimum of the likelihood function in polynomial time. If the haplotypes are not phased, finding the maximum value of the likelihood function is NP-hard. In this case, we define an alternative likelihood function which can be thought of as a relaxed likelihood function. We show that the maximum relaxed likelihood can be found in polynomial time and that the optimal solution of the relaxed likelihood approaches asymptotically to the haplotype frequencies in the population. In contrast to previous approaches, our algorithms are guaranteed to converge in polynomial time to a global maximum of the different likelihood functions. We compared the performance of our algorithm to the widely used program PHASE, and we found that our estimates are at least 10% more accurate than PHASE and about ten times faster than PHASE. Our techniques involve new algorithms in convex optimization. These algorithms may be of independent interest. Particularly, they may be helpful in other maximum likelihood problems arising from survey sampling.     

Analyses of gene frequencies

Models of variance components and their intraclass correlational equivalences are developed for genes falling into various categories of subdivisions within a population. Estimable functions are elaborated demonstrating that intraclass correlations can be estimated only relative to that for the least related genes in the informational system. The effects of different types of subdivisions-and of ignoring them-on the parameters are demonstrated. Small sample estimators are formulated for all of the parameters by three different methods, including both a weighted and an unweighted method of analysis of the variation among subpopulations. How estimators change with assumptions about the parameters is illustrated. Various tests of hypotheses are outlined in chi(2) and F-test terminology. Discussed are factors which may affect the correlations and the manner in which their effects are manifest, hopefully in clarification of some of the misconceptions that have arisen in this connection.     

Electromyography activity of vastus lateralis muscle during whole-body vibrations of different frequencies

The aim of this study was to analyze electromyography (EMG) responses of vastus lateralis muscle to different whole-body vibration frequencies. For this purpose, 16 professional women volleyball players (age, 23.9 +/- 3.6 years; height, 182.5 +/- 11.1 cm; weight, 78.4 +/- 5.6 kg) voluntarily participated in the study. Vibration treatment was administered while standing on a vibrating platform with knees bent at 100 degrees (Nemes Bosco-system, Rome, Italy). EMG root mean square (rms) and was recorded for 60 seconds while standing on the vibrating plate in the following conditions: no vibrations and 30-, 40-, and 50-Hz vibration frequencies in random order. The position was kept for 60 seconds in each treatment condition. EMGrms was collected from the vastus lateralis muscle of the dominant leg. Statistical analysis showed that, in all vibration conditions, average EMGrms activity of vastus lateralis was higher than in the no-vibration condition. The highest EMGrms was found at 30 Hz, suggesting this frequency as the one eliciting the highest reflex response in vastus lateralis muscle during whole-body vibrations in half-squat position. An extension of these studies to a larger population appears worthwhile to further elucidate the responsiveness of the neuromuscular system to whole-body vibrations administered through vibrating platforms and to be able to develop individual treatment protocols.     

Prediction of oligonucleotide frequencies based upon dinucleotide frequencies obtained from the nearest neighbor analysis.

A statistical method of predicting hexanucleotide frequencies is presented. The method requires dinucleotide frequencies which can be readily obtained by nearest neighbor analysis. The frequencies of 64 hexanucleotides of E. coli were estimated and compared well with those predicted by a third order Markov chain.     

Sex ratio of the mutation frequencies in haemophilia A: estimation and meta-analysis

Summary A hereditary disease with excess mortality such as haemophilia is maintained in the population by the occurrence of new cases, i.e. mutations. In haemophilia, mutations may arise in female or male ancestors of a new patient. The ratio of the mutation frequencies in males over females determines the prior risk of carriership of the mother of an isolated patient. An estimate of this prior risk is required for the application of Bayes' theorem to probability calculations in carriership testing. We have developed a method to estimate the sex ratio of the mutation frequencies; it does not depend on the assumption of genetic equilibrium, nor require an estimate of the reproductive fitness of haemophilia patients and carriers. Information from 462 patients with severe or moderately severe haemophilia A was gathered by postal questionnaires in a survey that included practically all Dutch haemophiliacs. Pedigree analysis was performed for the 189 patients of these 462, who were the first haemophiliacs in their family. By the maximum likelihood method, the ratio of the mutation frequencies in males and females was estimated at 2.1, with a 95% confidence interval of 0.7–6.7. In addition, we performed a meta-analysis of all published studies on the sex ratio of the mutation frequencies. When the results of six studies were pooled, it was estimated that mutations originated 3.1 times as often in males as in females. The 95% confidence interval was 1.9–4.9. This implies that 80% of mothers of an isolated patient are expected to be haemophilia carriers.     

Susceptibility of biallelic haplotype and genotype frequencies to genotyping error

With the availability of fast genotyping methods and genomic databases, the search for statistical association of single nucleotide polymorphisms with a complex trait has become an important methodology in medical genetics. However, even fairly rare errors occurring during the genotyping process can lead to spurious association results and decrease in statistical power. We develop a systematic approach to study how genotyping errors change the genotype distribution in a sample. The general M-marker case is reduced to that of a single-marker locus by recognizing the underlying tensor-product structure of the error matrix. Both method and general conclusions apply to the general error model; we give detailed results for allele-based errors of size depending both on the marker locus and the allele present. Multiple errors are treated in terms of the associated diffusion process on the space of genotype distributions. We find that certain genotype and haplotype distributions remain unchanged under genotyping errors, and that genotyping errors generally render the distribution more similar to the stable one. In case-control association studies, this will lead to loss of statistical power for nondifferential genotyping errors and increase in type I error for differential genotyping errors. Moreover, we show that allele-based genotyping errors do not disturb Hardy-Weinberg equilibrium in the genotype distribution. In this setting we also identify maximally affected distributions. As they correspond to situations with rare alleles and marker loci in high linkage disequilibrium, careful checking for genotyping errors is advisable when significant association based on such alleles/haplotypes is observed in association studies.     

Blood-protein allele frequencies and phylogenetic relationships in Macaca: A review

Allele-frequency data have been assembled for 35 blood-protein loci in 17 of 19 recognized species of Macaca based on 29 published electrophoretic studies; studies of inbred captive colonies have been excluded. Data for 22 polymorphic loci are tabulated in detail for 43 geographic populations of these species. Calculated F_ST values provide a measure of intergroup genetic differentiation at various hierarchical levels—troop, locality, province, country or island, species, species group; polymorphism indices measure genetic variation. The greatest intraspecific genetic differentiation occurs at the level of island populations within species. The pattern of genetic variation among island populations appears to be relictual, suggesting that the reduced genetic variability of island populations of macaques is a result of postisolation genetic drift rather than founder effect. Interspecific relationships were investigated by means of a jackknifed Fitch-Margoliash algorithm, using Papio as outgroup. Phylogenetic inferences based on morphology and zoogeography. The reduced genetic variability that frequently characterizes insular macaque populations complicates phylogenetic interpretation of blood-protein evidence.