A robust statistical method for association-based eQTL analysis

Background

It has been well established that theoretical kernel for recently surging genome-wide association study (GWAS) is statistical inference of linkage disequilibrium (LD) between a tested genetic marker and a putative locus affecting a disease trait. However, LD analysis is vulnerable to several confounding factors of which population stratification is the most prominent. Whilst many methods have been proposed to correct for the influence either through predicting the structure parameters or correcting inflation in the test statistic due to the stratification, these may not be feasible or may impose further statistical problems in practical implementation.

Methodology

We propose here a novel statistical method to control spurious LD in GWAS from population structure by incorporating a control marker into testing for significance of genetic association of a polymorphic marker with phenotypic variation of a complex trait. The method avoids the need of structure prediction which may be infeasible or inadequate in practice and accounts properly for a varying effect of population stratification on different regions of the genome under study. Utility and statistical properties of the new method were tested through an intensive computer simulation study and an association-based genome-wide mapping of expression quantitative trait loci in genetically divergent human populations.

Results/Conclusions

The analyses show that the new method confers an improved statistical power for detecting genuine genetic association in subpopulations and an effective control of spurious associations stemmed from population structure when compared with other two popularly implemented methods in the literature of GWAS.     

Diatoms from two macro-tidal mudflats in Chignecto Bay,Upper Bay of Fundy,New Brunswick,Canada

Mudflat research is dispersed among several fields (ecology, sedimentology), each with its own focus and methodology. Consequently, although the volume of mudflat literature is considerable, our understanding of mudflat ecology remains fragmented. For example, little is known about the structure of microbial communities outside Western Europe. Here we present the first North American specific composition and densities of live mudflat diatoms and relate them to properties of their environment on two closely located flats. The two flats (Daniel’s and Buck’s) were similar until the mid–1980s. After this time the biological and sedimentary environment on Buck’s Flats began to change and resulted in a precipitous decline of the keystone invertebrate Corophium volutator (Pallas). The specific diatom composition on each of the two flats examined was still very similar. Tychoplanktonic diatoms were numerically dominant on both flats. The flats differed significantly in the relative contribution of epipelic diatoms, which were about an order of magnitude greater on Buck’s Flats. CCA analysis suggests that very few of these species exist within their optimal habitat. Some of the differences appeared small, but were statistically and biologically significant. Daniel’s Flats sediments had a 30% larger mean grain size, less water and organic carbon compared to Buck’s Flats sediments. Buck’s Flats had more variable depths of the oxygenated layer, often with anoxic inclusions throughout. Daniel’s Flats supported more C. volutator, while Buck’s Flats contained greater densities of diatoms. The importance of preserving environmental conditions (sedimentary and biotic) prevailing on flats such as Danielȁ9s Flat in order to foster populations of Corophium at a level necessary to support foraging migratory shorebirds is also discussed.     

Zooplankton Communities of a Dammed Estuary in the Bay of Fundy,Canada

The upper estuary of the macrotidal Petitcodiac River, New Brunswick, Canada, was converted to a freshwater impoundment by construction of a causeway in 1968. Thirty years later, zooplankton community structure in the impoundment was characteristic of a disturbed ecosystem. The depauperate zooplankton consisted of a mixture of freshwater and marine/brackish taxa, but was not typical of regional estuaries or lakes. The causeway dam was an obstacle to fish migration, and several anadromous species that would formerly have been represented in the ichthyoplankton were absent. The invertebrate plankton community was dominated by rotifers, likely as a result of frequent water level fluctuations, and highly suspended sediment levels in the water column. Estuarine/marine calanoids (Eurytemora affinis, Temora longicornis, Centropages typicus, Tortanus discaudatus), the mysid Neomysis americana, and Cancer crab zoeae were collected in fresh water up to 14 km upstream of the causeway.     

Amphipods, isopods and surface currents: a case for passive dispersal in the Bay of Fundy, Canada

Six species of isopods and 18 species of amphipods were collectedin the neuston of the Bay of Fundy and adjacent waters. Collectionswere made over a grid of stations covering 2.4x10⁴ km² duringthree spring, three summer and two autumn surveys. No isopodsand only five species of amphipods were found in spring surveys.Isopods and amphipods were diverse and plentiful in the neustonin summer and autumn. Dominant isopods were Idotea baltica andI.metallica, and dominant amphipods were Calliopius laeviusculusand Parathemisto gaudichaudi. Amphipods and isopods reach theneuston of the Bay of Fundy in three ways. Idotea metallica,the only euneustonic species present, was probably advectedinto the Bay of Fundy from southern waters in summer, and didnot appear to overwinter in the Bay. Most species, includingI.baltica, were collected with drifting littoral vegetation,and we suggest that transport by surface currents is an importantfactor in dispersal of some shoreline crustaceans. Midwaterplankton, such as Parathemisto gaudichaudi, reached the neustoneither by advection in upwelling waters or by an extension oftheir normal diel vertical distribution.     

The Recent Terebratulina Community in the rocky subtidal zone of the Bay of Fundy, Canada

A distinctive rocky subtidal benthic community (the Terebratulina Community) is described from the Bay of Fundy, Canada. It is shown to consist of three closely intcrspersed sub-communities: a cavity sub-community, characterised by chitons, coelenterates, brachiopods, bryozoans, chordates and annelids; a rock-face subcommunity, similar in composition but enriched in brachiopods and sponges; and an upper-surface subcommunity, dominated by algae, chitons, bivalves and echinoids.
Comparison with recently described Jurassic, Cretaceous and Recent (Mediterranean) hard-ground communities suggests a relative constancy in composition, in terms of higher taxa, since the Mesozoic. Development of these (sub-)communities occurs wherever crevice or cavity systems on hard substrates lead to microenvironments differentiated mainly on the basis of water energy and light.
The composition and trophic structure of the community and the life habits of Terebratulina septentrionalis (Couthouy) are related to aspects of the environment. Marked differences in composition between the living cavity sub-community and the death assemblage in the sediments are shown to be due to differential preservation, fragmentation, population dynamics and limited local transportation.     

Nutrient availability reduced in older rural impoundments in coastal Bay of Fundy,Canada

The caddisfly species Micropterna lateralis is an abundant representative of limnephilids in intermittent streams. Yet, its basic life history characteristics and adaptations related to environmental factors, such as stream drying, are comparatively understudied. Here, we investigated larval growth and metabolic energy reserves (glycogen, triglycerides) through development in their natural habitat. We concentrated on the larval development because this period represents the important phase of energy accumulation necessary for growth, metamorphosis and embryogenesis. Besides larval physiology, female adults were studied in terms of ovarian maturation. Our results indicate that adult females lack an imaginal diapause, which is otherwise often observed in intermittent stream-inhabiting Limnephilidae. Further, M. lateralis is univoltine and exhibits a relatively fast larval development with five distinct instars, of which four are characterised here (instars II–V). Accrual of biomass occurs in final instars, where a high amount of glycogen is accumulated. Lipid concentrations, on the other hand, are kept constant in final stages and slightly lower than in preceding instars. This dominance of glycogen in final instars found in M. lateralis is highly unusual in insects and of potential adaptive significance for the species’ ability to exploit intermittent habitats.     

Behavioral Response of Corophium volutator to Shorebird Predation in the Upper Bay of Fundy,Canada

Predator avoidance is an important component of predator-prey relationships and can affect prey availability for foraging animals. Each summer, the burrow-dwelling amphipod Corophium volutator is heavily preyed upon by Semipalmated Sandpipers (Calidris pusilla) on mudflats in the upper Bay of Fundy, Canada. We conducted three complementary studies to determine if adult C. volutator exhibit predator avoidance behavior in the presence of sandpipers. In a field experiment, we monitored vertical distribution of C. volutator adults in bird exclosures and adjacent control plots before sandpipers arrived and during their stopover. We also made polymer resin casts of C. volutator burrows in the field throughout the summer. Finally, we simulated shorebird pecking in a lab experiment and observed C. volutator behavior in their burrows. C. volutator adults were generally distributed deeper in the sediment later in the summer (after sandpipers arrived). In August, this response was detectably stronger in areas exposed to bird predation than in bird exclosures. During peak predator abundance, many C. volutator adults were beyond the reach of feeding sandpipers (>1.5 cm deep). However, burrow depth did not change significantly throughout the summer. Detailed behavioral observations indicated that C. volutator spent more time at the bottom of their burrow when exposed to a simulated predator compared to controls. This observed redistribution suggests that C. volutator adults move deeper into their burrows as an anti-predator response to the presence of sandpipers. This work has implications for predators that feed on burrow-dwelling invertebrates in soft-sediment ecosystems, as density may not accurately estimate prey availability.     

A robust meta-classification strategy for cancer detection from MS data

We propose a novel method for phenotype identification involving a stringent noise analysis and filtering procedure followed by combining the results of several machine learning tools to produce a robust predictor. We illustrate our method on SELDI-TOF MS prostate cancer data (http://home.ccr.cancer.gov/ncifdaproteomics/ppatterns.asp). Our method identified 11 proteomic biomarkers and gave significantly improved predictions over previous analyses with these data. We were able to distinguish cancer from non-cancer cases with a sensitivity of 90.31% and a specificity of 98.81%. The proposed method can be generalized to multi-phenotype prediction and other types of data (e.g., microarray data).     

Genetic isolation of populations of the gammaridean amphipod, Corophium volutator, in the Bay of Fundy, Canada

Selection experiments suggest that evolutionary modifications in amphipod demography can respond to local environmental changes and that local races of amphipods may be common. We tested this hypothesis in mudflat populations of Corophium volutator in the Bay of Fundy, Canada. Due to the unique topography of the Bay of Fundy, distinctive environmental conditions are prevalent in different branches of the Bay, while the impact of shorebird predation has also been shown to vary between populations. Several hypotheses have been suggested to explain ecological evidence which indicates that Corophium volutator (Pallas), a common amphipod crustacean, exhibits extensive life history variation in Bay of Fundy populations. We used RAPD-PCR techniques to examine populations of C. volutator in an investigation of genetic isolation in marine environments. Our data suggest that variation in selection pressures have played a significant role in the genetic divergence of populations of C. volutator in the Bay of Fundy.     

Evidence of exposure to Brucella sp. in harbor porpoises (Phocoena phocoena) from the Bay of Fundy, Canada

Novel strains of Brucella recently have been discovered in marine mammals. To investigate Brucella exposure and infection in a general population of cetaceans, blood and tissue samples were collected and analyzed from wild harbor porpoises (Phocoena phocoena) incidentally caught in fishing gear in the Bay of Fundy, Canada. Two of 170 (1.2%) animals had detectable antibodies against Brucella, but no organisms were isolated from genital swabs or tissues from 22 and 8 porpoises, respectively. Genetic analysis of inflamed testes from 20 animals yielded no amplification of Brucella DNA. This is the first evidence of exposure to Brucella in porpoises from the western North Atlantic, and the prevalence is much lower than documented for conspecifics from the eastern North Atlantic.     

A new statistical method for haplotype reconstruction from population data

Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.     

The impact of scallop drags on sea urchin populations and benthos in the Bay of Fundy,Canada

The fishery for the green sea urchin (Strongylocentrotus droebachiensis) began in New Brunswick in the late 1980s in response to increasing demand from Asian markets, primarily Japan. Fishing was initiated by members of the scallop industry and the harvesting practices were based on familiar fishing gear (scallop drags or dredges) and similar operations occurring simultaneously in Maine. Because of the potential impact of scallop gear on the shallow water populations in areas not traditionally fished, a study was initiated in 1993 to document (1) the proportion of sea urchins damaged during the harvesting operation, (2) the impact on and subsequent recovery time of the associated benthic flora and epifauna, and (3) the impacts on the bottom substrate. Two sites were chosen for the study based on a split-plot design with a control and experimental plot at each site. In each experimental plot, a towing lane was created parallel to shore. Divers used a fixed line transect method to survey the control and treatment plots prior to and after the harvesting operation done with commercial scallop Digby drags. Further diver-based surveys were done 3 and 6 months later. Results showed a significant decrease in sea urchin densities and an increase in the number of broken sea urchin tests after the harvesting operation at the Passamaquoddy Bay and Grand Manan sites (3–15%). On both sites, there were significant changes in the density of mobile predators such as lobsters, crabs, whelks and sculpins. Lobster density declined to zero after dragging, but the lack of body parts suggested they moved out of the area. Whelks were observed to move into each of the experimental areas, likely in response to probable increase in available food. The dragging operation increased the breakage rate of the kelp, Laminaria longicruris. From the study we concluded that there were short-term impacts from dragging, but the observable effects on the bottom from the single dragging event were gone in less than 3 months. The longer-term effects of dragging were unknown.     

A statistical framework for differential network analysis from microarray data

Background  

It has been long well known that genes do not act alone; rather groups of genes act in consort during a biological process. Consequently, the expression levels of genes are dependent on each other. Experimental techniques to detect such interacting pairs of genes have been in place for quite some time. With the advent of microarray technology, newer computational techniques to detect such interaction or association between gene expressions are being proposed which lead to an association network. While most microarray analyses look for genes that are differentially expressed, it is of potentially greater significance to identify how entire association network structures change between two or more biological settings, say normal versus diseased cell types.     

A statistical method for predicting classical HLA alleles from SNP data

Genetic variation at classical HLA alleles is a crucial determinant of transplant success and susceptibility to a large number of infectious and autoimmune diseases. However, large-scale studies involving classical type I and type II HLA alleles might be limited by the cost of allele-typing technologies. Although recent studies have shown that some common HLA alleles can be tagged with small numbers of markers, SNP-based tagging does not offer a complete solution to predicting HLA alleles. We have developed a new statistical methodology to use SNP variation within the region to predict alleles at key class I (HLA-A, HLA-B, and HLA-C) and class II (HLA-DRB1, HLA-DQA1, and HLA-DQB1) loci. Our results indicate that a single panel of approximately 100 SNPs typed across the region is sufficient for predicting both rare and common HLA alleles with up to 95% accuracy in both African and non-African populations. Furthermore, we show that HLA alleles can be successfully predicted by using previously genotyped SNPs that are within the MHC and that had not been chosen for their ability to predict HLA alleles, such as those included on genome-wide products. These results indicate that our methodology, combined with an extended database of reference haplotypes, will facilitate large-scale experiments, including disease-association studies and vaccine trials, in which detailed information about HLA type is valuable.     

Littoral communities and zonation on rocky shores in the Bay of Fundy, Canada: an area of high tidal range

The Bay of Fundy, on the east coast of Canada, has a maximum tidal range slightly higher than that of the Bristol Channel and similar environmental conditions, but a more extreme climate. However, the littoral community, despite the common presence of many species, differs greatly. Fundy shores show universal domination by Ascopkyllum nodosum under all exposure conditions and its biomass is very high. Funis vesiculosus is common but its distribution is unrelated to exposure. Fucoid algae normally cover all but a few percent of the midlittoral. As a consequence of this intertidal primary primary productivity is very high and a protected sub-canopy environment very extensive. The standard littoral zones do show a typical pattern but respond only slightly to exposure. Many typical and important species show constant zonation under alt exposure conditions. Typical of this group are A. nodosum and the other fucoid algae. Although the high tidal range does reduce the effect of wave action, this factor alone does not explain the results since they are not repeated in the Bristol Channel. Differences in the suite of herbivores, particularly the absence of Patella species in Fundy, is considered to be an equally important causative factor. Also significant is the modifying effect of the heavy algal canopy itself. Clearance experiments have shown that dominance by A. nodosum is not restored within 10 years and that herbivory, especially by littorinids and limpets, does play a critical role in succession.     

A micro-computer program for statistical analysis of data from twin studies

A program of statistical processing of data obtained while examining twins is described. Transformed algorithms, directions for programme use and a control model are presented.     

A Matched Pairs Selection method for the analysis of abundance data with many zero values

Abstract. A simple method is described to analyze plant species abundance data with many zero values. To investigate the impact of an environmental factor on rare species, two subsets of sampling plots are selected pair-wise from the original data set. They differ in the value of the particular factor under consideration but are similar with respect to all other factors. Subsequently, the botanical composition of these subsets, including rare species, is compared using non-parametric tests. An example is given from a study on ditch bank vegetation. Some limitations, and a method for taking into account the dependence of the statistical tests, are discussed.     

A simple method for statistical analysis of intensity differences in microarray-derived gene expression data

Background  

Microarray experiments offer a potent solution to the problem of making and comparing large numbers of gene expression measurements either in different cell types or in the same cell type under different conditions. Inferences about the biological relevance of observed changes in expression depend on the statistical significance of the changes. In lieu of many replicates with which to determine accurate intensity means and variances, reliable estimates of statistical significance remain problematic. Without such estimates, overly conservative choices for significance must be enforced.     

Spatial attachment-site preferences of macroectoparasites on Atlantic sturgeons Acipenser oxyrinchus in Minas Basin, Bay of Fundy, Canada

Although parasite habitat preference is well studied, it is rarely rigorously evaluated statistically because of many zero intensities. Attachment-site preference and intensities of 2 macroectoparasite species ( Caligus elongatus and Calliobdella vivida ) of Atlantic sturgeon, Acipenser oxyrinchus Mitchill, in Minas Basin, Bay of Fundy, Canada, were characterized with the use of zero-inflated negative binomial statistical models that included a fork-length offset to control for body size. Three other parasites were encountered, sometimes in high numbers on various body sites, but too few counts overall prevented construction of meaningful statistical models. Of 26 sturgeons, prevalence of (1) C. elongatus (Copepoda) was 85%, mainly on caudal fins and nonfin body sites; (2) C. vivida (Hirudinea) was 81%, mainly on the pelvic and pectoral fins, and dorsal and ventral-lateral body sites; (3) Dichelesthium oblongum (Copepoda) was 31% within the gills or burrowed into the musculature at the base of fins; (4) Argulus stizostethii (Crustacea: Branchiura) was 8%; and (5) Nitzschia sturionis (Monogenea) was 12%. Only D. oblongum was associated with visible damage, mainly as lesions on gills and soft tissues. Characterizing parasite prevalences within the Bay of Fundy is important because some parasites affect fish health and population biology.     

A robust method for the detection of linkage in familial disease.

A nonparametric method for the detection of critical genes associated with familial disease was presented. The method involves the detection of deviations from expected identity by descent distributions at polymorphic marker loci for affected sib pairs. The method thus avoids the difficulties arising from incomplete penetrance, variable age of onset and other complications present in other forms of linkage analysis. The theoretical properties of method were worked out in detail for two important cases -- that of an incompletely penetrant recessive or incompletely penetrant dominant critical autosomal gene linked to a codominant marker locus. An easily implementable decision rule for the detection of linkage was proposed, and its operating characteristics for a variety of alternative hypothesis were obtained.