Paediatric talus fractures are rare injuries resulting from axial loading of the talus against the anterior tibia with the foot in dorsiflexion. Skeletally immature bone is less brittle, with higher elastic resistance than adult bone, thus the paediatric talus can sustain higher forces before fractures occur. However, displaced paediatric talus fractures and those associated with high-energy trauma have been associated with complications including avascular necrosis, arthrosis, delayed union, neurapraxia and the need for revision surgery. The authors present the rare case of a talar neck fracture in a skeletally immature young girl, initially missed on radiological review. However, clinical suspicion on the part of the emergency physician, repeat examination and further radiographic imaging revealed this rare paediatric injury.

DNA methyltransferases establish methylation patterns in cells and transmit these patterns over cell generations, thereby influencing each cell's epigenetic states. Three primary DNA methyltransferases have been identified in mammals: DNMT1, DNMT3A and DNMT3B. Extensive in vitro studies have investigated key properties of these enzymes, namely their substrate specificity and processivity. Here we study these properties in vivo, by applying novel statistical analysis methods to double-stranded DNA methylation patterns collected using hairpin-bisulfite PCR. Our analysis fits a novel Hidden Markov Model (HMM) to the observed data, allowing for potential bisulfite conversion errors, and yields statistical estimates of parameters that quantify enzyme processivity and substrate specificity. We apply this model to methylation patterns established in vivo at three loci in humans: two densely methylated inactive X (Xi)-linked loci ([Formula: see text] and [Formula: see text]), and an autosomal locus ([Formula: see text]), where methylation densities are tissue-specific but moderate. We find strong evidence for a high level of processivity of DNMT1 at [Formula: see text] and [Formula: see text], with the mean association tract length being a few hundred base pairs. Regardless of tissue types, methylation patterns at [Formula: see text] are dominated by DNMT1 maintenance events, similar to the two Xi-linked loci, but are insufficiently informative regarding processivity to draw any conclusions about processivity at that locus. At all three loci we find that DNMT1 shows a strong preference for adding methyl groups to hemi-methylated CpG sites over unmethylated sites. The data at all three loci also suggest low (possibly 0) association of the de novo methyltransferases, the DNMT3s, and are consequently uninformative about processivity or preference of these enzymes. We also extend our HMM to reanalyze published data on mouse DNMT1 activities in vitro. The results suggest shorter association tracts (and hence weaker processivity), and much longer non-association tracts than human DNMT1 in vivo.

Genetic effects on gene regulation make a substantial contribution to phenotypic diversity, yet their mechanisms remain elusive. Here, we discuss the potential insights to be gained from mapping gene-environment interactions at regulatory polymorphisms (i.e., genetic variation that affects gene expression under specific environmental conditions). We highlight a novel statistical method to identify specific patterns of gene-environment interaction at these regulatory polymorphisms. Reviewing its application to a study that mapped gene expression in the presence and absence of glucocorticoids, we discuss the mechanistic insights that this approach provides.

PURPOSE: To identify health-related behaviors associated with potentially harmful dietary supplements (DS)- body building (BB), weight loss (WL) and performance enhancing (PE), explore common reasons and sources of information for DS use. METHODS: Based on the 2005 Survey of 16,146 U.S. military personnel, BB users were dichotomized as yes (regular use - taking any supplement of BB at least once a week in past 12 months) or no; similarly defined for WL and PE. Weighted logistic regression models are used. RESULTS: BB, WL and PE were used by 19.4%, 17.0%, and 8.0% of participants, respectively. Significantly more users were overweight or obese: BMI ≥25 (vs. BMI<25); heavy drinkers (vs. abstainers); and users of taking steroids in their lifetime (vs. not). Most common reasons of BB, WL, and PE users wanted to increase muscle mass, lose weight, and improve physical performance (BB: 45.8%, WL: 54.8%, PE: 38.5%). Fewer than 30% discussed dietary supplements use with their healthcare providers. The leading source of dietary supplements information (BB: 27.8%, WL: 23.6%, PE: 30.0%) was magazines. CONCLUSIONS: The dietary supplements: BB, WL and PE were used by significant proportions of service members, and associated with risk-taking behaviors that may affect overall military readiness and public health.

Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. These panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 Genomes Project produce larger and more diverse reference sets, which led us to develop an alternative framework. Our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. This approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. Using data from HapMap 3, we show that our framework produces accurate results in a wide range of human populations. We also use data from the Malaria Genetic Epidemiology Network (MalariaGEN) to provide recommendations for imputation-based studies in Africa. We demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. Genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. New methodology from this study is implemented in the IMPUTE2 software package.

Mapping of expression quantitative trait loci (eQTLs) is an important technique for studying how genetic variation affects gene regulation in natural populations. In a previous study using Illumina expression data from human lymphoblastoid cell lines, we reported that cis-eQTLs are especially enriched around transcription start sites (TSSs) and immediately upstream of transcription end sites (TESs). In this paper, we revisit the distribution of eQTLs using additional data from Affymetrix exon arrays and from RNA sequencing. We confirm that most eQTLs lie close to the target genes; that transcribed regions are generally enriched for eQTLs; that eQTLs are more abundant in exons than introns; and that the peak density of eQTLs occurs at the TSS. However, we find that the intriguing TES peak is greatly reduced or absent in the Affymetrix and RNA-seq data. Instead our data suggest that the TES peak observed in the Illumina data is mainly due to exon-specific QTLs that affect 3' untranslated regions, where most of the Illumina probes are positioned. Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation.

The mapping of expression quantitative trait loci (eQTLs) has emerged as an important tool for linking genetic variation to changes in gene regulation. However, it remains difficult to identify the causal variants underlying eQTLs, and little is known about the regulatory mechanisms by which they act. Here we show that genetic variants that modify chromatin accessibility and transcription factor binding are a major mechanism through which genetic variation leads to gene expression differences among humans. We used DNase I sequencing to measure chromatin accessibility in 70 Yoruba lymphoblastoid cell lines, for which genome-wide genotypes and estimates of gene expression levels are also available. We obtained a total of 2.7 billion uniquely mapped DNase I-sequencing (DNase-seq) reads, which allowed us to produce genome-wide maps of chromatin accessibility for each individual. We identified 8,902 locations at which the DNase-seq read depth correlated significantly with genotype at a nearby single nucleotide polymorphism or insertion/deletion (false discovery rate = 10%). We call such variants 'DNase I sensitivity quantitative trait loci'(dsQTLs). We found that dsQTLs are strongly enriched within inferred transcription factor binding sites and are frequently associated with allele-specific changes in transcription factor binding. A substantial fraction (16%) of dsQTLs are also associated with variation in the expression levels of nearby genes (that is, these loci are also classified as eQTLs). Conversely, we estimate that as many as 55% of eQTL single nucleotide polymorphisms are also dsQTLs. Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation.

ABSTRACT: BACKGROUND: Expression quantitative trait loci (eQTLs) are likely to play an important role in the genetics of complex traits; however, their functional basis remains poorly understood. Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb. RESULTS: We use a Bayesian hierarchical model to estimate the enrichment of eQTLs in a wide variety of regulatory annotations. We find that approximately 40% of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions. Analysis of core promoter regions shows that eQTLs also frequently disrupt some known core promoter motifs but, surprisingly, are not enriched in other well-known motifs such as the TATA box. We also show that information from regulatory annotations alone, when weighted by the hierarchical model, can provide a meaningful ranking of the SNPs that are most likely to drive gene expression variation. CONCLUSIONS: Our study demonstrates how regulatory annotation and the association signal derived from eQTL-mapping can be combined into a single framework. We used this approach to further our understanding of the biology that drives human gene expression variation, and of the putatively causal SNPs that underlie it.

BACKGROUND:: Budesonide (BUD) is being used in pediatric Crohn's disease (CD) because it is believed to have the potential to reduce corticosteroid-related toxicity. However, little data are available describing its use. AIM:: To describe BUD use in an inception cohort of pediatric patients with CD. METHODS:: Data were derived from the prospective Pediatric IBD Collaborative Research Group Registry established in 2002 in North America. Use of BUD in children with CD was examined. RESULTS:: BUD was used in 119/932 (13%) of children with newly diagnosed CD, with 56/119 (47%) starting BUD ≤30 days of diagnosis (26/56 with ileum and/or ascending colon (IAC) disease). BUD was used as monotherapy (9%), in combination with 5ASA (77%) or in combination with immunomodulators (IM)(43%). Forty-three percent (24/56) went on to receive conventional corticosteroid at some point following their first BUD course. For the 63/119 (53%) who started BUD beyond the diagnosis period 51/63 (81%) also received prednisone, with BUD used as a means of weaning from prednisone in 17/63 (27%). Patients with IAC disease who received BUD ≤30 days of diagnosis were just as likely to have received conventional corticosteroids by one year as were those who did not receive BUD ≤30 days of diagnosis. Two thirds (77/119) of patients received budesonide for ≤6 months. CONCLUSIONS:: BUD is being used among newly diagnosed pediatric CD patients, although the majority do not have disease limited to the IAC. BUD monotherapy was rare, and further data is required to better define the role of BUD in the treatment of pediatric CD.

Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of non-human primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps towards addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 non-human primates. Of the non-human primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5,721 genes per species, and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerels sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have therefore strong potential to achieve long-term success.