The impact of rare and low-frequency genetic variants in common disease

Despite thousands of genetic loci identified to date, a large proportion of genetic variation predisposing to complex disease and traits remains unaccounted for. Advances in sequencing technology enable focused explorations on the contribution of low-frequency and rare variants to human traits. Here we review experimental approaches and current knowledge on the contribution of these genetic variants in complex disease and discuss challenges and opportunities for personalised medicine

Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.

BACKGROUND: This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. Experimental procedures for this are slow and costly, and computational methods are hard, because they lack positional information. RESULTS: We present a novel statistical method, the "fluffy-tail test", to recognise regulatory DNA. We exploit one of the basic informational properties of regulatory DNA: abundance of over-represented transcription factor binding site (TFBS) motifs, although we do not look for specific TFBS motifs, per se . Though overrepresentation of TFBS motifs in regulatory DNA has been intensively exploited by many algorithms, it is still a difficult problem to distinguish regulatory from other genomic DNA. CONCLUSION: We show that, in the data used, our method is able to distinguish cis-regulatory modules by exploiting statistical differences between the probability distributions of similar words in regulatory and other DNA. The potential application of our method includes annotation of new genomic sequences and motif discovery.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding elements (CNEs) are associated with genes that coordinate development, and have been proposed to act as transcriptional enhancers. Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates. Results Here we report that nematode genomes contain an alternative set of CNEs that share sequence characteristics, but not identity, with their vertebrate counterparts. CNEs thus represent a very unusual class of sequences that are extremely conserved within specific animal lineages yet are highly divergent between lineages. Nematode CNEs are also associated with developmental regulatory genes, and include well-characterized enhancers and transcription factor binding sites, supporting the proposed function of CNEs as cis-regulatory elements. Most remarkably, 40 of 156 human CNE-associated genes with invertebrate orthologs are also associated with CNEs in both worms and flies. Conclusion A core set of genes that regulate development is associated with CNEs across three animal groups (worms, flies and vertebrates). We propose that these CNEs reflect the parallel evolution of alternative enhancers for a common set of developmental regulatory genes in different animal groups. This 're-wiring' of gene regulatory networks containing key developmental coordinators was probably a driving force during the evolution of animal body plans. CNEs may, therefore, represent the genomic traces of these 'hard-wired' core gene regulatory networks that specify the development of each alternative animal body plan.Published versio

Results of a survey among opioid addiction treatment providers on the importance of physical exercise

Background: Physical exercise has significant benefits for mental and physical health. The Federal Office of Public Health in Switzerland defined exercise as a medium-term treatment goal in the manual of heroin-assisted treatment. Methods: Sixty-four opioid agonist treatment providers and specialized psychosocial treatment centers across the German-speaking part of Switzerland were asked to fill in a brief, self-developed questionnaire to find out whether exercise programs are offered and what they consist of. The questionnaire additionally addressed the caregivers’ assessment of their respec- tive treatment facilities importance to their patients, their attitude towards exercising programs, and the frequency of mentioning exercise in patient encounters. In addition, we asked what kind of sports programs caregivers would like to see introduced in their treatment services. Results: Fifty-one questionnaires were returned. According to the caregivers, 76% of patients considered their treatment facility to be the first point of contact in case of an emergency. Caregivers who deemed the provision of exercise programs more important also mentioned exercise more often in their patient encounters and motivated patients more often. While the importance of exercise programs was rated high by 45% of caregivers, only seven respondents reported that regular exercise has been implemented as part of their treatment services. The most com- mon suggestion of a sports program was (Nordic) walking, followed by yoga and endurance sports. Conclusions: There is a mismatch between what is recommended and known regarding cost effectiveness of physical exercise in general, any form of walking in opioid addiction treatment, and what is actually offered and put into practice. Since this intervention allows the inclusion of most patients regardless of their fitness level or health condition, the reasons for this mismatch remain elusive and should be further explored

An interactive genome browser of association results from the UK10K cohorts project.

UNLABELLED: High-throughput sequencing technologies survey genetic variation at genome scale and are increasingly used to study the contribution of rare and low-frequency genetic variants to human traits. As part of the Cohorts arm of the UK10K project, genetic variants called from low-read depth (average 7×) whole genome sequencing of 3621 cohort individuals were analysed for statistical associations with 64 different phenotypic traits of biomedical importance. Here, we describe a novel genome browser based on the Biodalliance platform developed to provide interactive access to the association results of the project. AVAILABILITY AND IMPLEMENTATION: The browser is available at http://www.uk10k.org/dalliance.html. Source code for the Biodalliance platform is available under a BSD license from http://github.com/dasmoth/dalliance, and for the LD-display plugin and backend from http://github.com/dasmoth/ldserv

A seismically induced onshore surge deposit at the KPg boundary, North Dakota

This work is licensed under a Creative Commons Attribution 4.0 International License.The most immediate effects of the terminal-Cretaceous Chicxulub impact, essential to understanding the global-scale environmental and biotic collapses that mark the Cretaceous–Paleogene extinction, are poorly resolved despite extensive previous work. Here, we help to resolve this by describing a rapidly emplaced, high-energy onshore surge deposit from the terrestrial Hell Creek Formation in Montana. Associated ejecta and a cap of iridium-rich impactite reveal that its emplacement coincided with the Chicxulub event. Acipenseriform fish, densely packed in the deposit, contain ejecta spherules in their gills and were buried by an inland-directed surge that inundated a deeply incised river channel before accretion of the fine-grained impactite. Although this deposit displays all of the physical characteristics of a tsunami runup, the timing (<1 hour postimpact) is instead consistent with the arrival of strong seismic waves from the magnitude Mw ∼10 to 11 earthquake generated by the Chicxulub impact, identifying a seismically coupled seiche inundation as the likely cause. Our findings present high-resolution chronology of the immediate aftereffects of the Chicxulub impact event in the Western Interior, and report an impact-triggered onshore mix of marine and terrestrial sedimentation—potentially a significant advancement for eventually resolving both the complex dynamics of debris ejection and the full nature and extent of biotic disruptions that took place in the first moments postimpact.Netherlands Organization for Scientific Research Grant 864.12.005United Kingdom Science and Technology Facilities Council (Grant STFC:ST/M001814/1

The influence of rare variants in circulating metabolic biomarkers.

Circulating metabolite levels are biomarkers for cardiovascular disease (CVD). Here we studied, association of rare variants and 226 serum lipoproteins, lipids and amino acids in 7,142 (discovery plus follow-up) healthy participants. We leveraged the information from multiple metabolite measurements on the same participants to improve discovery in rare variant association analyses for gene-based and gene-set tests by incorporating correlated metabolites as covariates in the validation stage. Gene-based analysis corrected for the effective number of tests performed, confirmed established associations at APOB, APOC3, PAH, HAL and PCSK (p<1.32x10-7) and identified novel gene-trait associations at a lower stringency threshold with ACSL1, MYCN, FBXO36 and B4GALNT3 (p<2.5x10-6). Regulation of the pyruvate dehydrogenase (PDH) complex was associated for the first time, in gene-set analyses also corrected for effective number of tests, with IDL and LDL parameters, as well as circulating cholesterol (pMETASKAT<2.41x10-6). In conclusion, using an approach that leverages metabolite measurements obtained in the same participants, we identified novel loci and pathways involved in the regulation of these important metabolic biomarkers. As large-scale biobanks continue to amass sequencing and phenotypic information, analytical approaches such as ours will be useful to fully exploit the copious amounts of biological data generated in these efforts

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

Methods for accurate identification of nucleotide and structural variation using de novo short read sequencing of mouse chromosomes are described

Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease.

Neutrophils play fundamental roles in innate immune response, shape adaptive immunity, and are a potentially causal cell type underpinning genetic associations with immune system traits and diseases. Here, we profile the binding of myeloid master regulator PU.1 in primary neutrophils across nearly a hundred volunteers. We show that variants associated with differential PU.1 binding underlie genetically-driven differences in cell count and susceptibility to autoimmune and inflammatory diseases. We integrate these results with other multi-individual genomic readouts, revealing coordinated effects of PU.1 binding variants on the local chromatin state, enhancer-promoter contacts and downstream gene expression, and providing a functional interpretation for 27 genes underlying immune traits. Collectively, these results demonstrate the functional role of PU.1 and its target enhancers in neutrophil transcriptional control and immune disease susceptibility