Analysis of Allelic Association: Estimation of the Power of the TDT

Analysis of allelic associations is an increasingly more widely used approach to fine mapping of genes of various diseases. To interpret the results correctly, it is necessary to estimate the power of the statistical test used. The principle of the analysis of associations and testing of hypothesis are described, and analytically obtained estimates of the power of the transmission disequilibrium test (TDT), one of the most popular methods of analysis of allelic associations, are presented. These estimates are applicable to arbitrary models of inheritance formulated in terms of genotypic relative risk. The proposed method is illustrated by analysis of the associations of idiopathic scoliosis and aggrecan gene alleles.     

The power of the transmission disequilibrium test (TDT) with both case-parent and control-parent trios

The transmission disequilibrium test (TDT) customarily uses affected children and their parents (often case-parent trios, TDTD). Control-parent trios are necessary to guard against spurious significant results due to segregation distortion but are not generally utilized in the identification of disease susceptibility loci (DSL). Controls are often easy to recruit and the TDT can easily be extended to include control-parent trios into the analyses with unrelated case-parent trios. We present an extension of the TDT (TDTDC) that incorporates unrelated cases and controls and their parents into a single analysis. We develop a simple and accurate analytical method for computing the statistical power of various TDT (e.g. the TDTD, TDTDC, TDTDC and TDTC that employ control-parent trios only) under any genetic model. We investigated the power of these TDT, and particularly compared the relative power of the TDTD and TDTDC. We found that the TDTDC is almost always more powerful than the TDTC and TDTD. The relative power of the TDTDC and TDTD depends largely upon a number of parameters identified in the study. This study provides a basis for efficient use of control-parent trios in DSL identification.     

Some criteria for the estimation of evoked potentials

The estimation of an evoked potential from an ensemble of observations is considered from the statistical point of view. In comparing different estimators it appears that the common mean square loss function is inappropriate in evoked potential studies. A modified loss function is proposed which is insensitive to overall scalling factors in the estimate. Using that loss function the properties of different estimators are explored and lines are indicated along which the estimation can be improved. Simulation examples illustrate the theoretical concepts. It is concluded that it is usually possible to improve on averaging, although comparison of the results of more advanced techniques to those of averaging always remains essential to avoid possibly erroneous interpretations.Until August 1984 visiting associate professor in Electrical Engineering and Neurology, University of Wisconsin, Department of Electrical and Computer Engineering, 1415 Johnson Drive, Madison, WI 53706, USA     

General equations for Pt, Ps, and the power of the TDT and the affected-sib-pair test

Several equations are highlighted here, whose algebraic symmetries and generality make them very useful for understanding and comparing the properties of the transmission disequilibrium test (TDT) and affected sib-pair test. Methods using the equations are also presented that yield precise estimates of sample sizes needed for genome scans or for testing a single candidate gene, and these power methods are shown to compare favorably with alternative approaches recently described by Knapp (1999) and by Tu and Whittemore (1999). Simple relationships are also noted that summarize the relative sample sizes required for equivalent power to detect association by the TDT or case-control designs. As single-nucleotide polymorphism (SNP) maps revolutionize the search for disease-causing genes, the equations should prove useful for planning and evaluating studies of linkage and association across a broad range of possible disease models and relationships between markers and linked disease loci.     

Analysis of the association of allelic variants of apolypoprotein E and interleukin 1 beta genes with multiple sclerosis in ethnic Tatars

Multiple sclerosis (MS) is a multifactorial disease of the central nervous system. The apolipoprotein E (APOE) and interleukin 1 beta (IL1B) genes are considered to be candidate genes of MS. The aim of the study was to examine the hypothesis of the importance of APOE and IL1B gene polymorphisms in MS development in ethnic Tatars. DNA samples isolated by phenol-chloroform extraction from peripheral blood of 383 ethnic Tatars (120 MS patients and 263 healthy donors) were studied. 112C/R and 158R/C APOE gene polymorphisms as well as -511T/C IL1B gene polymorphism were analyzed by polymerase chain reaction (PCR) followed by PCR product digestion by endonuclease. Odds ratio (OR) values were used for evaluation of the relative risk of alleles and(or) genotype combinations. It has been shown that APOE*2/*3 genotype is associated with low risk of the disease development (OR = 0.20) in women. A combined effect of APOE and IL1B allelic variants has been discovered indicating the increased risk of the disease development in the carriers of APOE*4 and IL1B*T/*T alleles (OR = 4.76).     

Analysis of the association of allelic variants of apolypoprotein E and interleukin 1 beta genes with multiple sclerosis in ethnic Tatars

Multiple sclerosis (MS) is a multifactorial disease of the central nervous system. The apolipoprotein E (APOE) and interleukin 1 β (IL1B) genes are considered to be candidate genes of MS. The aim of the study was to examine the hypothesis of the importance of APOE and IL1B gene polymorphisms in MS development in ethnic Tatars. DNA samples isolated by phenol-chloroform extraction from peripheral blood of 383 ethnic Tatars (120 MS patients and 263 healthy donors) were studied. 112C/R and 158R/C APOE gene polymorphisms as well as ?511T/C IL1B gene polymorphism were analyzed by polymerase chain reaction (PCR) followed by PCR product digestion by endonuclease. Odds ratio (OR) values were used for evaluation of the relative risk of alleles and(or) genotype combinations. It has been shown that APOE*2/*3 genotype is associated with low risk of the disease development (OR = 0.20) in women. A combined effect of APOE and IL1B allelic variants has been discovered indicating the increased risk of the disease development in the carriers of APOE*4 and IL1B*T/*T alleles (OR = 4.76).     

On selection criteria and estimation of parameters when the variance is heterogeneous

Summary Procedures for ranking candidates for selection and for estimating genetic and environmental parameters when variances are heterogeneous are discussed. The best linear unbiased predictor (BLUP) accounts automatically for heterogeneous variance provided that the covariance structure is known and that the assumptions of the model hold. Under multivariate normality BLUP allowing for heterogeneous variance maximizes expected genetic progress. Examples of application of BLUP to selection when residual or genetic variances are heterogeneous are given. Restricted maximum likelihood estimation of heterogeneous variances and covariances via the expectation-maximization algorithm is presented.     

Flower power: its association with bee power and floral functional morphology in papilionate legumes

Background and Aims

A test was made of the hypothesis that papilionate legume flowers filter pollinators according to their ability to exert strength to open flowers to access rewards. In addition, interactions with pollen vectors were expected to explain the structural complexity of the architecture of these flowers since operative flower strength may be determined by a combination of morphological traits which form part of an intrafloral functional module.

Methods

Six papilionate species were studied: Collaea argentina, Desmodium uncinatum, Galactia latisiliqua, Lathyrus odoratus, Spartium junceum and Tipuana tipu. Measurements were made of the strength needed to open keels and the strength that pollinators were capable of exerting. Morphological traits of all petals were also measured to determine which of them could be either mutually correlated or correlated with operative strength and moment of strength and participated in a functional module.

Key Results

It was observed that pollinators were capable in all cases of exerting forces higher and often several times higher than that needed to access floral rewards, and no association could be detected between floral operative strength and strength exerted by the corresponding pollinators. On the other hand, strong and significant correlations were found among morphometric traits and, of these, with operative strength and moment. This was particularly evident among traits of the keel and the wings, presumably involved in the functioning of the floral moveable mechanism.

Conclusions

Though visitors are often many times stronger than the operative strength of the flowers they pollinate, exceptionally weak bees such as Apis mellifera cannot open the strongest flowers. On the other hand, strong correlations among certain petal morphometric traits (particularly between the keel and wings) give support to the idea that an intrafloral module is associated with the functioning of the mechanism of these legume flowers. In addition, the highly significant correlations found across petals support the view of functional phenotypic integration transcending the ontogenetic organization of flower structure.     

Analysis of linkage and association of alleles of proinflammatory cytokines genes IL-6, IFNg and TNF with multiple sclerosis using transmission disequilibrium test (TDT)

Proinflammatory cytokines Interleukin-6 (IL-6), Interferon-gamma (IFNg) and Tumor necrosis factor (TNF) are known as participants of inflammation and play an important role in pathogenesis of multiple sclerosis (MS). Based on literature data about influence of SNPs G(-308)A of TNF gene, A(+874)T of IFNG gene and G(-174)C of IL-6 gene on production of these cytokines, we investigated association of these polymorphic sites with MS. Linkage and association of alleles of these genes with MS was analyzed by transmission disequilibrium test (TDT). In investigated group of 104 nuclear families of Russian ethnicity it was found that TNF* (-308)A allele transmitted from healthy heterozygous parents to affected children more frequently (p = 0.01). Linkage/association of IFNG and IL-6 alleles with MS was not revealed. Thus, data obtained indicate the participation of TNF gene in MS susceptibility in Russians.     

Rethinking resolution estimation in fluorescence microscopy: from theoretical resolution criteria to super-resolution microscopy

Science China Life Sciences - Resolution is undoubtedly the most important parameter in optical microscopy by providing an estimation on the maximum resolving power of a certain optical microscope....     

Polymorphism in the rhesus macaque (Macaca mulatta) NRAMP1 gene: lack of an allelic association to tuberculosis susceptibility

Although previous tuberculosis (TB) research has suggested that underlying genetic factors influence a host's response and ability to survive Mycobacterium infection, only recently has a gene been identified, the 'natural resistance-associated macrophage protein 1' (NRAMP1) gene, which provides a degree of natural resistance to infection by some Mycobacterium species. To date, however, the role that NRAMP1 may play in resistance to Mycobacterium infection has only been examined in mouse and man. Here, we present data generated at NRAMP1 among a group of rhesus macaques (Macaca mulatta) that were euthanized because of an outbreak of Mycobacterium tuberculosis during quarantine. Data were also generated on unrelated (and healthy) rhesus macaques in order to better determine the frequency and degree of genetic polymorphism within Macaca at the NRAMP1 locus. These data represent the first study designed to examine the role that NRAMP1 may play in TB susceptibility among rhesus macaques.     

Microbiologicaland immunological criteria for estimation of ureaplasmosis treatment efficacy in women

The role of surface and parietal vaginal microbiocenosis and immunoglobulins in development of infectious process, in prediction of resistance of causative microorganism to antibiotics and treatment efficacy was demonstrated on group of women with ureaplasmosis. Evaluation of anaerobic part of vaginal microbiota contemporary with its aerobic part reliably increased informative value of microbiological test in women with urogenital diseases. There are reasons to include interferon preparations into the complex therapy of ureaplasmosis.     

Simple deterministic identity-by-descent coefficients and estimation of QTL allelic effects in full and half sibs

Accurate and rapid methods for the detection of quantitative trait loci (QTLs) and evaluation of consequent allelic effects are required to implement marker-assisted selection in outbred populations. In this study, we present a simple deterministic method for estimating identity-by-descent (IBD) coefficients in full- and half-sib families that can be used for the detection of QTLs via a variance-component approach. In a simulated dataset, IBD coefficients among sibs estimated by the simple deterministic and Markov chain Monte Carlo (MCMC) methods with three or four alleles at each marker locus exhibited a correlation of greater than 0.99. This high correlation was also found in QTL analyses of data from an outbred pig population. Variance component analysis used both the simple deterministic and MCMC methods to estimate IBD coefficients. Both procedures detected a QTL at the same position and gave similar test statistics and heritabilities. The MCMC method, however, required much longer computation than the simple method. The conversion of estimated QTL genotypic effects into allelic effects for use in marker-assisted selection is also demonstrated.     

The estimator of the optimal measure of allelic association: mean, variance and probability distribution when the sample size tends to infinity

The allelic association or linkage disequilibrium between two loci is a parameter of fundamental interest in modern population genetics for evolutionary inference and association mapping studies. Among the many measures available, the optimal measure of allelic association rho presents a strong evolutionary theory basis and is modeled on the physical distance along the chromosome with the Malécot equation for isolation by distance. Moreover, rho is equal to the absolute value of D', the standardized measure of gametic disequilibrium. We studied here the statistical properties of the rho sample estimator. We derived its asymptotic probability distribution and showed that it is neither asymptotically normal nor unbiased when rho=0 or when allelic frequencies are equal at both loci, in contrast to previous claims. This asymptotic study leads to propose a new test for absence of linkage disequilibrium. We compared it to Pearson's Chi2 test for independence in a contingency table and showed by simulations that the range in power of these two tests depends on the sign of D'. The new test outperformed slightly the Chi2 test, when D', polarized with respect to major alleles, is negative. Finally, we derived the asymptotic bias and information of the rho estimator that are due to the experimental sampling and showed by simulation that its bias is large in small samples. The consequences of these findings on applications using the rho measure are then discussed in particular for constructing LD unit maps, and call for a revised statistical treatment.