Family-based association analysis with ordered categorical phenotypes, covariates and interactions

Genetic association analyses of family-based studies with ordered categorical phenotypes are often conducted using methods either for quantitative or for binary traits, which can lead to suboptimal analyses. Here we present an alternative likelihood-based method of analysis for single nucleotide polymorphism (SNP) genotypes and ordered categorical phenotypes in nuclear families of any size. Our approach, which extends our previous work for binary phenotypes, permits straightforward inclusion of covariate, gene-gene and gene-covariate interaction terms in the likelihood, incorporates a simple model for ascertainment and allows for family-specific effects in the hypothesis test. Additionally, our method produces interpretable parameter estimates and valid confidence intervals. We assess the proposed method using simulated data, and apply it to a polymorphism in the c-reactive protein (CRP) gene typed in families collected to investigate human systemic lupus erythematosus. By including sex interactions in the analysis, we show that the polymorphism is associated with anti-nuclear autoantibody (ANA) production in females, while there appears to be no effect in males.

Genetic association analysis of vitamin D pathway with obesity traits

Objective:Observational studies have examined the link between vitamin D deficiency and obesity traits. Some studies have reported associations between vitamin D pathway genes such as VDR, GC and CYP27B1 with body mass index (BMI) and waist circumference (WC); however, the findings have been inconsistent. Therefore, we investigated the involvement of vitamin D metabolic pathway genes in obesity-related traits in a large population-based study.Methods:We undertook a comprehensive analysis between 100 tagging single nucleotide polymorphisms (tagSNPs) in genes encoding for DHCR7, CYP2R1, VDBP, CYP27B1, CYP27A1, CYP24A1, VDR and RXRG, and obesity traits in 5224 participants (aged 45 years) in the 1958 British birth cohort (1958BC). We further extended our analyses to investigate the associations between SNPs and obesity traits using the summary statistics from the GIANT (Genetic Investigation of Anthropometric Traits) consortium (n=123 865).Results:In the 1958BC (n=5224), after Bonferroni correction, none of the tagSNPs were associated with obesity traits except for one tagSNP from CYP24A1 that was associated with waist-hip ratio (WHR) (rs2296239, P=0.001). However, the CYP24A1 SNP was not associated with BMI-adjusted WHR (WHRadj) in the 1958BC (rs2296239, P=1.00) and GIANT results (n=123 865, P=0.18). There was also no evidence for an interaction between the tagSNPs and obesity on BMI, WC, WHR and WHRadj in the 1958BC. In the GIANT consortium, none of the tagSNPs were associated with obesity traits.Conclusions:Despite a very large study, our findings suggest that the vitamin D pathway genes are unlikely to have a major role in obesity-related traits in the general population.

A genome wide association study of mathematical ability reveals an association at chromosome 3q29, a locus associated with autism and learning difficulties: a preliminary study

Mathematical ability is heritable, but few studies have directly investigated its molecular genetic basis. Here we aimed to identify specific genetic contributions to variation in mathematical ability. We carried out a genome wide association scan using pooled DNA in two groups of U.K. samples, based on end of secondary/high school national academic exam achievement: high (n = 419) versus low (n = 183) mathematical ability while controlling for their verbal ability. Significant differences in allele frequencies between these groups were searched for in 906,600 SNPs using the Affymetrix GeneChip Human Mapping version 6.0 array. After meeting a threshold of p<1.5×10-5, 12 SNPs from the pooled association analysis were individually genotyped in 542 of the participants and analyzed to validate the initial associations (lowest p-value 1.14 ×10-6). In this analysis, one of the SNPs (rs789859) showed significant association after Bonferroni correction, and four (rs10873824, rs4144887, rs12130910 rs2809115) were nominally significant (lowest p-value 3.278 × 10-4). Three of the SNPs of interest are located within, or near to, known genes (FAM43A, SFT2D1, C14orf64). The SNP that showed the strongest association, rs789859, is located in a region on chromosome 3q29 that has been previously linked to learning difficulties and autism. rs789859 lies 1.3 kbp downstream of LSG1, and 700 bp upstream of FAM43A, mapping within the potential promoter/regulatory region of the latter. To our knowledge, this is only the second study to investigate the association of genetic variants with mathematical ability, and it highlights a number of interesting markers for future study.

A genome-wide association meta-analysis identifies new childhood obesity loci

Multiple genetic variants have been associated with adult obesity and a few with severe obesity in childhood; however, less progress has been made in establishing genetic influences on common early-onset obesity. We performed a North American, Australian and European collaborative meta-analysis of 14 studies consisting of 5,530 cases (≥95th percentile of body mass index (BMI)) and 8,318 controls (<50th percentile of BMI) of European ancestry. Taking forward the eight newly discovered signals yielding association with P < 5 × 10(-6) in nine independent data sets (2,818 cases and 4,083 controls), we observed two loci that yielded genome-wide significant combined P values near OLFM4 at 13q14 (rs9568856; P = 1.82 × 10(-9); odds ratio (OR) = 1.22) and within HOXB5 at 17q21 (rs9299; P = 3.54 × 10(-9); OR = 1.14). Both loci continued to show association when two extreme childhood obesity cohorts were included (2,214 cases and 2,674 controls). These two loci also yielded directionally consistent associations in a previous meta-analysis of adult BMI(1).

Meta-analysis of the INSIG2 association with obesity including 74,345 individuals: does heterogeneity of estimates relate to study design?

The INSIG2 rs7566605 polymorphism was identified for obesity (BMI> or =30 kg/m(2)) in one of the first genome-wide association studies, but replications were inconsistent. We collected statistics from 34 studies (n = 74,345), including general population (GP) studies, population-based studies with subjects selected for conditions related to a better health status ('healthy population', HP), and obesity studies (OB). We tested five hypotheses to explore potential sources of heterogeneity. The meta-analysis of 27 studies on Caucasian adults (n = 66,213) combining the different study designs did not support overall association of the CC-genotype with obesity, yielding an odds ratio (OR) of 1.05 (p-value = 0.27). The I(2) measure of 41% (p-value = 0.015) indicated between-study heterogeneity. Restricting to GP studies resulted in a declined I(2) measure of 11% (p-value = 0.33) and an OR of 1.10 (p-value = 0.015). Regarding the five hypotheses, our data showed (a) some difference between GP and HP studies (p-value = 0.012) and (b) an association in extreme comparisons (BMI> or =32.5, 35.0, 37.5, 40.0 kg/m(2) versus BMI<25 kg/m(2)) yielding ORs of 1.16, 1.18, 1.22, or 1.27 (p-values 0.001 to 0.003), which was also underscored by significantly increased CC-genotype frequencies across BMI categories (10.4% to 12.5%, p-value for trend = 0.0002). We did not find evidence for differential ORs (c) among studies with higher than average obesity prevalence compared to lower, (d) among studies with BMI assessment after the year 2000 compared to those before, or (e) among studies from older populations compared to younger. Analysis of non-Caucasian adults (n = 4889) or children (n = 3243) yielded ORs of 1.01 (p-value = 0.94) or 1.15 (p-value = 0.22), respectively. There was no evidence for overall association of the rs7566605 polymorphism with obesity. Our data suggested an association with extreme degrees of obesity, and consequently heterogeneous effects from different study designs may mask an underlying association when unaccounted for. The importance of study design might be under-recognized in gene discovery and association replication so far.

Proceedings of the Ninth Annual Conference of the British Association for Biological Anthropology and Osteoarchaeology, Department of Archaeology, University of Reading

The Proceedings of the Ninth Annual Conference of the British Association for Biological Anthropology and Osteoarchaeology (BABAO) held at the University of Reading in 2007. Contents: 1) A life course perspective of growing up in medieval London: evidence of sub-adult health from St Mary Spital (London) (Rebecca Redfern and Don Walker); 2) Preservation of non-adult long bones from an almshouse cemetery in the United States dating to the late nineteenth to the early twentieth centuries (Colleen Milligan, Jessica Zotcavage and Norman Sullivan); 3) Childhood oral health: dental palaeopathology of Kellis 2, Dakhleh, Egypt. A preliminary investigation (Stephanie Shukrum and JE Molto); 4) Skeletal manifestation of non-adult scurvy from early medieval Northumbria: the Black Gate cemetery, Newcastle-upon-Tyne (Diana Mahoney-Swales and Pia Nystrom); 5) Infantile cortical hyperostosis: cases, causes and contradictions (Mary Lewis and Rebecca Gowland); 6) Biological Anthropology Tuberculosis of the hip in the Victorian Britain (Benjamin Clarke and Piers Mitchell); 7) The re-analysis of Iron Age human skeletal material from Winnall Down (Justine Tracey); 8) Can we estimate post-mortem interval from an individual body part? A field study using sus scrofa (Branka Franicevec and Robert Pastor); 9) The expression of asymmetry in hand bones from the medieval cemetery at Écija, Spain (Lisa Cashmore and Sonia Zakrezewski); 10) Returning remains: a curator’s view (Quinton Carroll); 11) Authority and decision making over British human remains: issues and challenges (Piotr Bienkowski and Malcolm Chapman); 12) Ethical dimensions of reburial, retention and repatriation of archaeological human remains: a British perspective (Simon Mays and Martin Smith); 13) The problem of provenace: inaccuracies, changes and misconceptions (Margaret Clegg); 14) Native American human remains in UK collections: implications of NAGPRA to consultation, repatriation, and policy development (Myra J Giesen); 15) Repatriation – a view from the receiving end: New Zealand (Nancy Tayles).

Soil moisture mediates association between the winter North Atlantic Oscillation and summer growth in the Park Grass Experiment

Several aspects of terrestrial ecosystems are known to be associated with the North Atlantic Oscillation (NAO) through effects of the NAO on winter climate, but recently the winter NAO has also been shown to be correlated with the following summer climate, including drought. Since drought is a major factor determining grassland primary productivity, the hypothesis was tested that the winter NAO is associated with summer herbage growth through soil moisture availability, using data from the Park Grass Experiment at Rothamsted, UK between 1960 and 1999. The herbage growth rate, mean daily rainfall, mean daily potential evapotranspiration (PE) and the mean and maximum potential soil moisture deficit (PSMD) were calculated between the two annual cuts in early summer and autumn for the unlimed, unfertilized plots. Mean and maximum PSMD were more highly correlated than rainfall or PE with herbage growth rate. Regression analysis showed that the natural logarithm of the herbage growth rate approximately halved for a 250 mm increase in maximum PSMD over the range 50-485 mm. The maximum PSMD was moderately correlated with the preceding winter NAO, with a positive winter NAO index associated with greater maximum PSMD. A positive winter NAO index was also associated with low herbage growth rate, accounting for 22% of the interannual variation in the growth rate. It was concluded that the association between the winter NAO and summer herbage growth rate is mediated by the PSMD in summer.

Analysis of the SDS−Lysozyme binding isotherm

A scheme to describe SDS−lysozyme complex formation has been proposed on the basis of isothermal titration calorimetry (ITC) and FTIR spectroscopy data. ITC isotherms are convoluted and reveal a marked effect of both SDS and lysozyme concentration on the stoichiometry of the SDS−lysozyme complex. The binding isotherms have been described with the aid of FTIR spectroscopy in terms of changes in the lysozyme structure and the nature of the SDS binding. At low SDS concentrations, ITC isotherms feature an exothermic region that corresponds to specific electrostatic binding of SDS to positively charged amino acid residues on the lysozyme surface. This leads to charge neutralization of the complex and precipitation. The number of SDS molecules that bind specifically to lysozyme is approximately 8, as determined from our ITC isotherms, and is independent of lysozyme solution concentration. At high SDS concentrations, hydrophobic cooperative association dominates the binding process. Saturated binding stoichiometries as a molar ratio of SDS per molecule of lysozyme range from 220:1 to 80:1, depending on the lysozyme solution concentration. A limiting value of 78:1 has been calculated for lysozyme solution concentrations above 0.25 mM.

Association between ovarian follicle development and pregnancy rates in dairy cows undergoing spontaneous oestrous cycles

Ovarian follicle development continues in a wave-like manner during the bovine oestrous cycle giving rise to variation in the duration of ovulatory follicle development. The objectives of the present study were to determine whether a relationship exists between the duration of ovulatory follicle development and pregnancy rates following artificial insemination (AI) in dairy cows undergoing spontaneous oestrous cycles, and to identify factors influencing follicle turnover and pregnancy rate and the relationship between these two variables. Follicle development was monitored by daily transrectal ultrasonography from 10 days after oestrus until the subsequent oestrus in 158 lactating dairy cows. The cows were artificially inseminated following the second observed oestrus and pregnancy was diagnosed 35 days later. The predominant pattern of follicle development was two follicle waves (74.7%) with three follicle waves in 22.1% of oestrous cycles and four or more follicle waves in 3.2% of oestrous cycles. The interval from ovulatory follicle emergence to oestrus (EOI) was 3 days longer (P < 0.0001) in cows with two follicle waves than in those with three waves. Ovulatory follicles from two-wave oestrous cycles grew more slowly but were approximately 2 mm larger (P < 0.0001) on the day of oestrus. Twin ovulations were observed in 14.2% of oestrous cycles and occurred more frequently (P < 0.001) in three-wave oestrous cycles; consequently EOI was shorter in cows with twin ovulations. Overall, 57.0% of the cows were diagnosed pregnant 35 days after AI. Linear logistic regression analysis revealed an inverse relationship between EOI and the proportion of cows diagnosed pregnant, among all cows (n = 158; P < 0.01) and amongst those with single ovulations (n = 145; P < 0.05). Mean EOI was approximately I day shorter (P < 0.01) in cows that became pregnant than in non-pregnant cows; however, pregnancy rates did not differ significantly among cows with different patterns of follicle development. These findings confirm and extend previous observations in pharmacologically manipulated cattle and show, for the first time, that in dairy cows undergoing spontaneous oestrous cycles, natural variation in the duration of post-emergence ovulatory follicle development has a significant effect on pregnancy rate, presumably reflecting variation in oocyte developmental competence.

Comparative analysis by protocol and key of seed storage behaviour of sixty Vietnamese tree species

Seed storage behaviour of 5 1 native and 9 introduced tree species in Vietnam was investigated using a brief protocol developed to aid biodiversity conservation in circumstances where little is known about the seeds. Of the 60 species, 34 appeared to show orthodox (Acacia auriculaeformis, Adenanthera pavonina, Afzelia xylocarpa, Bauhinia purpurea, Callistemon lanceolatus, Cananga odorata, Canarium nigrum, Cassia fistula, Cassia javanica, Cassia splendida, Chukrasia tabularis, Dalbergia bariaensis, Dialium cochinchinensis, Diospyros mollis, Diospyros mun, Dracuntomelon duperreanum, Erythrophleum fordii, Khaya senegalensis, Lagerstroemia speciosa, Leucaena leucocephala, Livistona cochinchinensis, Markhamia stipulata, Melaleuca cajuputi, Millettia ichthyotona, Peltophorum pterocarpum, Peltophorum tonkinensis, Pinus khasya, Pinus massoniana, Pinus merkusii, Pterocarpus macrocarpus, Sindora siamensis, Sophora tonkinense, Sterculia foetida, Swietenia macrophylla), 13 recalcitrant (Avicennia alba, Beilschmiedia roxburghiana, Caryota mitis, Dimocarpus sp., Diospyros malabarica, Dipterocarpus chartaceus, Dypsis pinnatifrons, Hopea odorata, Lithocarpus gigantophylla, Machilus odoratissimus, Melanorrhoea laccifera, Melanorrhea usitata, Syzygium cinereum) and 13 intermediate (Anisoptera cochinchinensis, Aphanamixis polystachya, Averrhoa carambola, Carissa carandas, Chrysopylum cainito, Cinnamomum camphora, Citrofortunella microcarpa, Citrus grandis var. grandis, Elaeis guineensis, Hydnocarpus anthelmintica, Madhuca floribunda, Manilkara achras, Mimusops elengi) seed storage behaviour. A double-criteria key to estimate likely seed storage behaviour showed good agreement with the above: the key can reduce the workload of seed storage behaviour identification considerably.

Predicting feed quality - chemical analysis and in vitro evaluation

As the ideal method of assessing the nutritive value of a feedstuff, namely offering it to the appropriate class of animal and recording the production response obtained, is neither practical nor cost effective a range of feed evaluation techniques have been developed. Each of these balances some degree of compromise with the practical situation against data generation. However, due to the impact of animal-feed interactions over and above that of feed composition, the target animal remains the ultimate arbitrator of nutritional value. In this review current in vitro feed evaluation techniques are examined according to the degree of animal-feed interaction. Chemical analysis provides absolute values and therefore differs from the majority of in vitro methods that simply rank feeds. However, with no host animal involvement, estimates of nutritional value are inferred by statistical association. In addition given the costs involved, the practical value of many analyses conducted should be reviewed. The in sacco technique has made a substantial contribution to both understanding rumen microbial degradative processes and the rapid evaluation of feeds, especially in developing countries. However, the numerous shortfalls of the technique, common to many in vitro methods, the desire to eliminate the use of surgically modified animals for routine feed evaluation, paralleled with improvements in in vitro techniques, will see this technique increasingly replaced. The majority of in vitro systems use substrate disappearance to assess degradation, however, this provides no information regarding the quantity of derived end-products available to the host animal. As measurement of volatile fatty acids or microbial biomass production greatly increases analytical costs, fermentation gas release, a simple and non-destructive measurement, has been used as an alternative. However, as gas release alone is of little use, gas-based systems, where both degradation and fermentation gas release are measured simultaneously, are attracting considerable interest. Alternative microbial inocula are being considered, as is the potential of using multi-enzyme systems to examine degradation dynamics. It is concluded that while chemical analysis will continue to form an indispensable part of feed evaluation, enhanced use will be made of increasingly complex in vitro systems. It is vital, however, the function and limitations of each methodology are fully understood and that the temptation to over-interpret the data is avoided so as to draw the appropriate conclusions. With careful selection and correct application in vitro systems offer powerful research tools with which to evaluate feedstuffs. (C) 2003 Elsevier B.V. All rights reserved.

A likelihood ratio appropach to family-based association studies with covariates

We introduce a procedure for association based analysis of nuclear families that allows for dichotomous and more general measurements of phenotype and inclusion of covariate information. Standard generalized linear models are used to relate phenotype and its predictors. Our test procedure, based on the likelihood ratio, unifies the estimation of all parameters through the likelihood itself and yields maximum likelihood estimates of the genetic relative risk and interaction parameters. Our method has advantages in modelling the covariate and gene-covariate interaction terms over recently proposed conditional score tests that include covariate information via a two-stage modelling approach. We apply our method in a study of human systemic lupus erythematosus and the C-reactive protein that includes sex as a covariate.

Urban mammals: what does the future hold? An analysis of the factors affecting patterns of use of residential gardens in Great Britain

1Urban areas are predicted to grow significantly in the foreseeable future because of increasing human population growth. Predicting the impact of urban development and expansion on mammal populations is of considerable interest due to possible effects on biodiversity and human-wildlife conflict. 2The British government has recently announced a substantial housing programme to meet the demands of its growing population and changing socio-economic profile. This is likely to result in the construction of high-density, low-cost housing with small residential gardens. To assess the potential effects of this programme, we analysed the factors affecting the current pattern of use of residential gardens by a range of mammal species using a questionnaire distributed in wildlife and gardening magazines and via The Mammal Society. 3Twenty-two species/species groups were recorded. However, the pattern of garden use by individual species was limited, with only six species/species groups (bats, red fox Vulpes vulpes, grey squirrel Sciurus carolinensis, hedgehog Erinaceus europaeus, mice, voles) recorded as frequent visitors to > 20% of gardens in the survey. 4There was a high degree of association between the variables recorded in the study, such that it was difficult to quantify the effects of individual variables. However, all species/species groups appeared to be negatively affected by the increased fragmentation and reduced proximity of natural and semi-natural habitats, decreasing garden size and garden structure, but to differing degrees. Patterns of garden use were most clearly affected by house location (city, town, village, rural), with garden use declining with increasing urbanization for the majority of species/species groups, except red foxes and grey squirrels. Increasing urbanization is likely to be related to a wide range of interrelated factors, any or all of which may affect a range of mammal species. 5Overall, the probable effects of the planned housing development programme in Britain are not likely to be beneficial to mammal populations, although the pattern of use examined in this study may represent patterns of habitat selection by species rather than differences in distribution or abundance. Consequently, additional data are required on the factors affecting the density of species within urban environments.

Numbers of antral follicles during follicular waves in cattle: Evidence for high variation among animals, very high repeatability in individuals, and an inverse association with serum follicle-stimulating hormone concentrations

The extent, causes, and physiological significance of the variation in number of follicles growing during ovarian follicular waves in human beings and cattle are unknown. Therefore, the present study examined the variability and repeatability in numbers of follicles 3 mm or greater in diameter during the follicular waves in bovine estrous cycles, and we determined if the variation in number of follicles during waves was associated with alterations in secretion of FSH, estradiol, inhibin, and insulin-like growth factor I (IGF-I). Dairy cattle were subjected to twice-daily ultrasound analysis to count total number of antral follicles 3 mm or greater in diameter throughout 138 different follicular waves. In another study, blood samples were taken at frequent intervals from cows that consistently had low or very high numbers of follicles during waves and were subjected to immunoassays. Results indicate the following: First, despite an approximately sevenfold variation in number of follicles during waves among animals and marked differences in age, stage of lactation, and season of the year, a very highly repeatable (0.95) number of follicles 3 mm or greater in diameter is maintained during the ovulatory and nonovulatory follicular waves of individuals. Second, variation in number of follicles 3 mm or greater in diameter during waves and the inverse association of number of follicles during waves with FSH are not directly explained by alterations in the patterns of secretion of estradiol, inhibin, or IGF-I. Third, ovarian ultrasound analysis can be used reliably by investigators to identify cattle that consistently have low or high numbers of follicles during waves, thus providing a novel experimental model to determine the causes and physiological significance of the high variation in antral follicle number during follicular waves among single-ovulating species, such as cattle or humans.