Association Testing Strategy for Data from Dense Marker Panels

Genome wide association studies have been usually analyzed in a univariate manner. The commonly used univariate tests have one degree of freedom and assume an additive mode of inheritance. The experiment-wise significance of these univariate statistics is obtained by adjusting for multiple testing. Next generation sequencing studies, which assay 10-20 million variants, are beginning to come online. For these studies, the strategy of additive univariate testing and multiple testing adjustment is likely to result in a loss of power due to (1) the substantial multiple testing burden and (2) the possibility of a non-additive causal mode of inheritance. To reduce the power loss we propose: a new method (1) to summarize in a single statistic the strength of the association signals coming from all not-very-rare variants in a linkage disequilibrium block and (2) to incorporate, in any linkage disequilibrium block statistic, the strength of the association signals under multiple modes of inheritance. The proposed linkage disequilibrium block test consists of the sum of squares of nominally significant univariate statistics. We compare the performance of this method to the performance of existing linkage disequilibrium block/gene-based methods. Simulations show that (1) extending methods to combine testing for multiple modes of inheritance leads to substantial power gains, especially for a recessive mode of inheritance, and (2) the proposed method has a good overall performance. Based on simulation results, we provide practical advice on choosing suitable methods for applied analyses.     

Test a clade in phylogenetic trees

We develop a new method for testing a portion of a tree (called a clade) based on multiple tests of many 4-taxon trees in this paper. This is particularly useful when the phylogenetic tree constructed by other methods have a clade that is difficult to explain from a biological point of view. The statement about the test of the clade can be made through the multiple P values from these individual tests. By controlling the familywise error rate or the false discovery rate (FDR), 4 different tree test methods are evaluated through simulation methods. It shows that the combination of the approximately unbiased (AU) test and the FDR-controlling procedure provides strong power along with reasonable type I error rate and less heavy computation.     

Sampling techniques and the use of Tang's procedure in insect population dynamics studies

Some calculations were performed usingTang 's method as an aid in planning experiments for studying the population dynamics of the Jeffrey pine beetle. The population dynamics studies were aimed at detecting the importance of specific effects, e. g., tree diameter, tree height. TheTang procedure is a method of estimating the sample size required to detect effects of a given magnitude with analysis of variance tests. Using this procedure some sample calculations were performed which indicated the sample size needed, and the efficacy of different strategies of improving the results, e. g., increasing the number of trees sampled versus increasing the area of the tree sampled. The statistical parameters used in the calculations were estimated from some preliminary sampling data. Use of this procedure is recommended in insect population studies as a method of optimally planning experiments, and as a method of making precise conclusions about the significance of specific effects.     

Evaluation of a rapid membrane enzyme immunoassay (Testpack HIV-1/HIV-2) at zonal, regional and district hospital laboratories in Tanzania

The performance of a rapid and simple membrane enzyme immunoassay for antibodies to HIV-1 and HIV-2 (Testpack HIV-1/HIV-2) was evaluated by testing 1000 sera from the Kilimanjaro region of Tanzania. A sensitivity of 100% (118/118 positives) and specificity of 95.1% were obtained following the manufacturer's procedure. The specificity was significantly enhanced to 97.2% (P = 0.026) by modifying the Testpack procedure by including an extra was after serum adsorption to the unit membrane. The testing of a single specimen could be completed in 8 min and up to 10 individual tests could be run simultaneously. There was complete agreement in interpretation when the results were read independently by two trained technicians. A built-in control insured against incorrect procedures or inactive reagents. In a subsequent field trial including 450 sera, one strongly reactive sample failed to be detected at a participating field hospital for unknown reasons. The Testpack reagents proved stable for up to one year at room temperature (25-30 degrees C). The data indicate that Testpack is suitable for the detection of serum antibodies to HIV and is especially applicable in laboratories with limited facilities. When used to test African sera which are known to produce a high degree of false positivity, an extra wash of the membrane after serum adsorption is recommended.     

Qualified testing of single-locus codominant inheritance using single tree progenies

In forest trees, classical techniques of studying modes of inheritance are usually not feasible due to the difficulty of performing controlled crosses. The limited information on inheritance extractable from readily available data, such as the large progenies collectable from single seed trees, must be compensated by the design of appropriately parameterized models. For this purpose, a system analytic approach is used to develop a new inferential framework for testing a single-locus codominant mode of inheritance of genetic traits using the inferred genotypes within progenies of single trees of inferred heterozygous genotype. Model assumptions are random gametic fusion between the local gamete pools and absence of postzygotic selection; ovule segregation distortion is allowed. The method yields estimates of the allele frequencies in both local gamete pools. Since tests of modes of inheritance must be tests of models rather than of parameters, the utility of the classical statistical testing procedures is limited, particularly concerning the qualification of a sampling method to attain a preassigned level of precision. Consistent application of this principle makes it possible to design qualified sampling methods prior to the actual experiment as well as to specify qualification levels for tests of completed experiments.     

Comparison of Methods for Coccidioidomycosis Complement Fixation

A Laboratory Branch Task Force of the National Communicable Disease Center has proposed a standardized complement fixation procedure (LBCF) and an adaptation of this to microtitration techniques (MT) as uniform methods for performing complement fixation (CF) tests. A common procedure should make CF results from one laboratory more comparable to another. In addition, it would be preferable if the common procedure reproduced the titer levels of a testing procedure which is to be replaced, particularly when valid clinical interpretations have been derived from the latter. Replicated sets of sera were tested by the LBCF, MT, and the standard Smith CF procedure for coccidioidomycosis. Results with all three procedures were highly reproducible within an acceptable one-tube variation of a twofold dilution series, but the frequency of one-tube variations was greater with the MT method than with the other two. There was no statistical difference in the titers obtained with the Smith and LBCF procedures, but there was a significant difference when the MT results were compared to those with the Smith method. The LBCF method should be acceptable as a standardized and uniform CF procedure for coccidioidomycosis, subject to comparative testing between different laboratories.     

Nonparametric tests for continuous covariate effects with multistate survival data

SUMMARY: In clinical trials and observational studies, it is often of scientific interest to evaluate the effects of covariates on complex multistate event probabilities. With discrete covariates, nonparametric tests may be constructed using estimates of the relevant quantities. With continuous covariates, a common approach is to arbitrarily discretize the covariates, which may lead to substantial information loss. Another strategy is to formulate the covariate effects in a regression model. Model-based tests may have either low power or be biased under misspecification. We propose nonparametric tests not requiring arbitrary discretization. The tests involve integrals of estimates continuously indexed by dichotomizations of the covariates. General asymptotic results are derived under null and alternative hypotheses, and verified using empirical process theory in several special cases. The tests are consistent under stochastic ordering, which arises naturally with multistate data. A novel nonparametric measure of covariate effect is studied as a natural byproduct of the testing procedure. Simulation studies and two real data analyses demonstrate the gains of the new testing procedure over those based either on categorization or on regression models.     

Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

The rate at which a given site in a gene sequence alignment evolves over time may vary. This phenomenon--known as heterotachy--can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here, we describe a phylogenetic mixture model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our 'pattern-heterogeneity' mixture model, applying it to simulated data and five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of 'significance' such as the Akaike or Bayesian information criterion tests, or Bayes factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch-length information. These include molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data.     

Construction of linear invariants in phylogenetic inference.

An analytical method is presented for constructing linear invariants. All linear invariants of a k-species tree can be derived from those of (k-1)-species trees using this method. The new method is simpler than that of Cavender, which relies on numerical computations. Moreover, the new method provides a convenient tool to study the relationships between linear invariants of the same tree or of different trees. All linear invariants of trees of up to five species are derived in this study. For four species, there are 16 independent linear invariants for each of the three possible unrooted trees, 14 of which are shared by two unrooted trees and 12 of these are shared by all three unrooted trees; the last types of linear invariants can be used to construct tests on the assumptions about nucleotide substitutions. The number of linear invariants for a tree is found to increase rapidly with the number of species.     

Confidence intervals following group sequential tests in clinical trials

Tsiatis, Rosner, and Mehta (1984, Biometrics 40, 797-803) proposed a procedure for constructing confidence intervals following group sequential tests of a normal mean. This method is first extended for group sequential tests for which the sample sizes between interim analyses are not identical or the times are not equally spaced. Then properties of this confidence interval estimation procedure are studied by simulation. The extension accommodates the flexible procedure by Lan and DeMets (1983, Biometrika 70, 659-663) for constructing discrete group sequential boundaries to form a structure for monitoring and estimation following a class of group sequential tests. Finally, it is demonstrated how to combine the procedures by Lan and DeMets and by Tsiatis, Rosner, and Mehta using a FORTRAN program.     

Anticancer drug sensitivity testing using an oxygen electrode apparatus

Conventional anticancer drug sensitivity testing methods, such as succinate dehydrogenase inhibition (SDI), histoculture drug-response assay (HDRA) and collagen gel droplet embedded culture drug sensitivity testing (CD-DST), all require primary culturing and are extremely complex tests that require considerable time for analysis. A major drawback of these methods is that if culturing is not performed properly, ambiguous results are produced. Therefore, we developed an oxygen electrode apparatus that uses cellular metabolism as an indicator of anticancer drug sensitivity and investigated its usefulness in 29 breast cancer patients with the following histopathological classifications: papillotubular carcinoma (n= 15); solid tubular carcinoma (n= 6); and scirrhous carcinoma (n= 8). Comparison of anticancer drug sensitivity testing results obtained using the conventional HDRA method and those obtained using the oxygen electrode apparatus showed significant reproducibility between the two methods. In addition, similar anticancer drug sensitivity testing results using the oxygen electrode apparatus were obtained for in vivo testing of nude mice transplanted with established cancer cell lines. These findings suggest that the oxygen electrode apparatus is a useful procedure in anticancer drug sensitivity testing that provides better reproducibility and that is faster, more convenient, and less expensive than other testing methods.     

Sap flow rate and transpiration dynamics in the full-grown oak (Quercus robus L.) in floodplain forest exposed to seasonal floods as related to potential evapotranspiration and tree dimensions

Sap flow rate and transpiration dynamics were studied in the course of 3 years in a dominant tree species in the floodplain forest,i.e. in the full-grown oak (Quercus robur L.) tree, using the method of trunk heat balance devised by the authors. The investigations were carried out at a period at which regular and marked fluctuation in a relatively high water table usually occurred, culminating in seasonal flooding. High sap flow rate values in the tree were established under conditions of non-limiting water supply in soil (up to 400 kg per day or up to 39 000 kg per vegetation period) and characteristic daily flow curves (rounded with a large amplitude and with the maximum at noon), corresponding to those described theoretically. Relationships were inferred by means of which tree water consumption can be calculated under these conditions on the basis of data measured at meteorological stations. From these equations it follows that the transpiration of the tree canopy amounted to 80% of the potential evapotranspiration. The amount of the used daily tree water reserve was assessed to be 0.4 mm in the seasonal average. The transpiration coefficient reached in climatically distinct years the values of 400 to 700 of the increase in tree dry matter. The area of the so-called effective tree-crown ground plan approximated to the area determined geodetically. The results obtained are useful for both ecophysiological and hydrological studies. Some of the described procedures are convenient for the evaluation of functional tree dimensions and according to them also of the forest stand structure.     

The inheritance of organelle genes and genomes: patterns and mechanisms.

Unlike nuclear genes and genomes, the inheritance of organelle genes and genomes does not follow Mendel's laws. In this mini-review, I summarize recent research progress on the patterns and mechanisms of the inheritance of organelle genes and genomes. While most sexual eukaryotes show uniparental inheritance of organelle genes and genomes in some progeny at least part of the time, increasing evidence indicates that strictly uniparental inheritance is rare and that organelle inheritance patterns are very diverse and complex. In contrast with the predominance of uniparental inheritance in multicellular organisms, organelle genes in eukaryotic microorganisms, such as protists, algae, and fungi, typically show a greater diversity of inheritance patterns, with sex-determining loci playing significant roles. The diverse patterns of inheritance are matched by the rich variety of potential mechanisms. Indeed, many factors, both deterministic and stochastic, can influence observed patterns of organelle inheritance. Interestingly, in multicellular organisms, progeny from interspecific crosses seem to exhibit more frequent paternal leakage and biparental organelle genome inheritance than those from intraspecific crosses. The recent observation of a sex-determining gene in the basidiomycete yeast Cryptococcus neoformans, which controls mitochondrial DNA inheritance, has opened up potentially exciting research opportunities for identifying specific molecular genetic pathways that control organelle inheritance, as well as for testing evolutionary hypotheses regarding the prevalence of uniparental inheritance of organelle genes and genomes.     

Segregation analysis of congenital glaucoma: approach by two differential models.

To determine the mode of inheritance of congenital glaucoma, segregation analysis was performed using two different models: the transmission probability model and the mixed model. Whereas the latter, testing for monogenic inheritance in the presence of both monogenic and polygenic components, results in strong evidence for a major locus, the former, testing for Mendelian segregation at one locus, rejects this hypothesis. The differences in the results of these two models are discussed and are attributed to the underlying structure of each. Genetic heterogeneity of congenital glucoma is proposed.     

Integration and inheritance of transgenes in crop plants and trees

Transgene integration and inheritance have been investigated in a number of crop plants and few tree species. Transgene integration is predominantly a random process, whether mediated by Agrobacterium or particle bombardment. Depending on the genomic position of the integrated transgene and structure of the integration site as well as copy number of the transgene in the genome, its expression may be stable or variable. Therefore, integration patterns would affect the mode of transgene inheritance in plants, regardless of the method of gene transfer. So far, both Mendelian and non-Mendelian inheritance of transgenes has been reported across several generations (T1–T3) of crop plants. In few tree species (apple, poplar, plum, and American chestnut), mostly Mendelian inheritance of the transgenes has been observed in the T1 or BC1 generations. However, detailed studies in the transgenic papaya trees showed Mendelian segregation of the transgene in the T1 generation but non-Mendelian inheritance in the T2 generation. Variation in transgene inheritance was also detected in transgenic apple and plum trees. Long generation cycles in many economically important tree species preclude investigation of inheritance of transgenes in the tree progeny. Production of early flowering trees, either by genetic modification or by environmental modulation, would facilitate the study of transgene inheritance across generations of transgenic trees. In order to overcome problems of randomness of transgene integration, targeted transgene insertions by homologous or site-specific recombination or by designer recombinases or nucleases offer prospects for stable integration of transgenes in predetermined locations in the plant genome. And perhaps, that might provide a platform for stable expression and Mendelian inheritance of transgenes in plants.     

Further evidence for the increased power of LOD scores compared with nonparametric methods.

In genetic analysis of diseases in which the underlying model is unknown, "model free" methods-such as affected sib pair (ASP) tests-are often preferred over LOD-score methods, although LOD-score methods under the correct or even approximately correct model are more powerful than ASP tests. However, there might be circumstances in which nonparametric methods will outperform LOD-score methods. Recently, Dizier et al. reported that, in some complex two-locus (2L) models, LOD-score methods with segregation analysis-derived parameters had less power to detect linkage than ASP tests. We investigated whether these particular models, in fact, represent a situation that ASP tests are more powerful than LOD scores. We simulated data according to the parameters specified by Dizier et al. and analyzed the data by using a (a) single locus (SL) LOD-score analysis performed twice, under a simple dominant and a recessive mode of inheritance (MOI), (b) ASP methods, and (c) nonparametric linkage (NPL) analysis. We show that SL analysis performed twice and corrected for the type I-error increase due to multiple testing yields almost as much linkage information as does an analysis under the correct 2L model and is more powerful than either the ASP method or the NPL method. We demonstrate that, even for complex genetic models, the most important condition for linkage analysis is that the assumed MOI at the disease locus being tested is approximately correct, not that the inheritance of the disease per se is correctly specified. In the analysis by Dizier et al., segregation analysis led to estimates of dominance parameters that were grossly misspecified for the locus tested in those models in which ASP tests appeared to be more powerful than LOD-score analyses.     

Multiple testing on the directed acyclic graph of gene ontology

MOTIVATION: Current methods for multiplicity adjustment do not make use of the graph structure of Gene Ontology (GO) when testing for association of expression profiles of GO terms with a response variable. RESULTS: We propose a multiple testing method, called the focus level procedure, that preserves the graph structure of Gene Ontology (GO). The procedure is constructed as a combination of a Closed Testing procedure with Holm's method. It requires a user to choose a 'focus level' in the GO graph, which reflects the level of specificity of terms in which the user is most interested. This choice also determines the level in the GO graph at which the procedure has most power. We prove that the procedure strongly controls the family-wise error rate without any additional assumptions on the joint distribution of the test statistics used. We also present an algorithm to calculate multiplicity-adjusted P-values. Because the focus level procedure preserves the structure of the GO graph, it does not generally preserve the ordering of the raw P-values in the adjusted P-values. AVAILABILITY: The focus level procedure has been implemented in the globaltest and GlobalAncova packages, both of which are available on www.bioconductor.org.     

Presymptomatic testing for Huntington's disease in the United Kingdom. The United Kingdom Huntington's Disease Prediction Consortium.

OBJECTIVE--To evaluate the United Kingdom Huntington''s disease presymptomatic testing programme. DESIGN--Postal questionnaire survey to collect data on all tests performed by clinical genetics centres between 1987 and 1990. SETTING--Genetic centres providing presymptomatic testing in the United Kingdom. SUBJECTS--248 subjects at risk of Huntington''s disease who had presymptomatic testing at their request. MAIN OUTCOME MEASURES--Sex, age, prior risk, and risk after testing. RESULTS--The risk of carrying the Huntington disease gene was reduced for 151 (61%) of the applicants and raised for 97 (39%). 158 (64%) of the subjects were female and 90 (36%) male. The median age at which the results were given was 32.5 years. CONCLUSIONS--The demand for testing was lower than expected and may have reached its peak in 1990. The excess of low risk results was not fully explained by the age effect. All the genetics centres concerned have agreed a common service protocol which requires extensive pre-test counselling and post-test follow up. The worth of the procedure remains to be decided. The availability of a large body of pooled data from all the United Kingdom testing centres, which individually are likely to have only a few results, will form a valuable resource for monitoring the long term psychosocial impact of testing.     

A study of the cambial zone and conductive phloem of common beech (Fagus sylvatica L.) using an image analysis method

Quantification is a major problem when using histology to study the influence of ecological factors on tree structure. This paper presents a method to prepare and to analyse transverse sections of cambial zone and of conductive phloem in bark samples. The following paper (II) presents the automated measurement procedure. Part I here describes and discusses the preparation method, and the influence of tree age on the observed structure. Highly contrasted images of samples extracted at breast height during dormancy were analysed with an automatic image analyser. Between three young (38 years) and three old (147 years) trees, age-related differences were identified by size and shape parameters, at both cell and tissue levels. In the cambial zone, older trees had larger and more rectangular fusiform initials. In the phloem, sieve tubes were also larger, but their shape did not change and the area for sap conduction was similar in both categories. Nevertheless, alterations were limited, and demanded statistical analysis to be identified and ascertained. The physiological implications of the structural changes are discussed.     

The hydraulic system of trees: theoretical framework and numerical simulation

Empirical studies pose the problem of the physiological integration of the tree organism, which is also important on the scale of ecosystems. Recently, spatially distributed models emerged, which approach this problem by reflecting the close linkage between physiological processes and the structures of trees and tree stands. In the case of water flow, the tree organism can be regarded as hydraulic system and the branched tree architecture as hydraulic network. Previous models of the hydraulic system either did not take into account the network structure, or they had shortcomings regarding the translation of the underlying physiological assumptions by the discrete computation method. We have developed a theoretical framework which takes the form of a numerical simulation model of tree water flow. A discrete initial boundary value problem (IBVP) combines the phenomena of Darcy flow, water storage and conductivity losses in the hydraulic network. The software HYDRA computes the solution of the IBVP. The theoretical derivation and model tests corroborate the consistent translation of the physiological assumptions by the computational method. Simulation studies enabled us to formulate hypotheses on the following points: (1) differences in the hydraulic segmentation between Picea abies and Thuja occidentalis, (2) responses of the hydraulic system to rapid transpiration changes and to a scenario of drought stress, and (3) how these responses depend on architectural quantities of the trees. The simulation studies demonstrated our possibilities of deriving theoretically well-founded hypotheses about the functioning of the hydraulic system and its relation to system structure. The numerical simulation model is designed as a tool for structure-function studies, which is able to treat tree architecture as independent variable. The model supports the integration of data on tree level, and it can be used for computer experiments which quantify the dynamics of the hydraulic system according to the concepts of system theory. Copyright 1999 Academic Press.