GWAS of bone size yields twelve loci that also affect height, BMD, osteoarthritis or fractures

© 2019, The Author(s). Bone area is one measure of bone size that is easily derived from dual-energy X-ray absorptiometry (DXA) scans. In a GWA study of DXA bone area of the hip and lumbar spine (N ≥ 28,954), we find thirteen independent association signals at twelve loci that replicate in samples of European and East Asian descent (N = 13,608 – 21,277). Eight DXA area loci associate with osteoarthritis, including rs143384 in GDF5 and a missense variant in COL11A1 (rs3753841). The strongest DXA area association is with rs11614913[T] in the microRNA MIR196A2 gene that associates with lumbar spine area (P = 2.3 × 10−42, β = −0.090) and confers risk of hip fracture (P = 1.0 × 10−8, OR = 1.11). We demonstrate that the risk allele is less efficient in repressing miR-196a-5p target genes. We also show that the DXA area measure contributes to the risk of hip fracture independent of bone density

Eighty-eight variants highlight the role of T cell regulation and airway remodeling in asthma pathogenesis

Publisher's version (útgefin grein)Asthma is one of the most common chronic diseases affecting both children and adults. We report a genome-wide association meta-analysis of 69,189 cases and 702,199 controls from Iceland and UK biobank. We find 88 asthma risk variants at 56 loci, 19 previously unreported, and evaluate their effect on other asthma and allergic phenotypes. Of special interest are two low frequency variants associated with protection against asthma; a missense variant in TNFRSF8 and 3‘ UTR variant in TGFBR1. Functional studies show that the TNFRSF8 variant reduces TNFRSF8 expression both on cell surface and in soluble form, acting as loss of function. eQTL analysis suggests that the TGFBR1 variant acts through gain of function and together with an intronic variant in a downstream gene, SMAD3, points to defective TGFβR1 signaling as one of the biological perturbations increasing asthma risk. Our results increase the number of asthma variants and implicate genes with known role in T cell regulation, inflammation and airway remodeling in asthma pathogenesis.We thank the individuals who participated in this study and the staff at the Icelandic Patient Recruitment Center and the deCODE genetics core facilities. Further to all our colleagues who contributed to the data collection and phenotypic characterization of clinical samples as well as to the genotyping and analysis of the whole-genome association data. This research has been conducted using the UK biobank Resource under Application Number ‘24711’.Peer Reviewe

The genetic epidemiology of joint shape and the development of osteoarthritis

Congruent, low-friction relative movement between the articulating elements of a synovial joint is an essential pre-requisite for sustained, efficient, function. Where disorders of joint formation or maintenance exist, mechanical overloading and osteoarthritis (OA) follow. The heritable component of OA accounts for ~ 50% of susceptible risk. Although almost 100 genetic risk loci for OA have now been identified, and the epidemiological relationship between joint development, joint shape and osteoarthritis is well established, we still have only a limited understanding of the contribution that genetic variation makes to joint shape and how this modulates OA risk. In this article, a brief overview of synovial joint development and its genetic regulation is followed by a review of current knowledge on the genetic epidemiology of established joint shape disorders and common shape variation. A summary of current genetic epidemiology of OA is also given, together with current evidence on the genetic overlap between shape variation and OA. Finally, the established genetic risk loci for both joint shape and osteoarthritis are discussed

Variant ASGR1 associated with a reduced risk of coronary artery disease

BACKGROUND: Several sequence variants are known to have effects on serum levels of non-high-density lipoprotein (HDL) cholesterol that alter the risk of coronary artery disease. METHODS: We sequenced the genomes of 2636 Icelanders and found variants that we then imputed into the genomes of approximately 398,000 Icelanders. We tested for association between these imputed variants and non-HDL cholesterol levels in 119,146 samples. We then performed replication testing in two populations of European descent. We assessed the effects of an implicated loss-of-function variant on the risk of coronary artery disease in 42,524 case patients and 249,414 controls from five European ancestry populations. An augmented set of genomes was screened for additional loss-of-function variants in a target gene. We evaluated the effect of an implicated variant on protein stability. RESULTS: We found a rare noncoding 12-base-pair (bp) deletion (del12) in intron 4 of ASGR1, which encodes a subunit of the asialoglycoprotein receptor, a lectin that plays a role in the homeostasis of circulating glycoproteins. The del12 mutation activates a cryptic splice site, leading to a frameshift mutation and a premature stop codon that renders a truncated protein prone to degradation. Heterozygous carriers of the mutation (1 in 120 persons in our study population) had a lower level of non-HDL cholesterol than noncarriers, a difference of 15.3 mg per deciliter (0.40 mmol per liter) (P=1.0×10(-16)), and a lower risk of coronary artery disease (by 34%; 95% confidence interval, 21 to 45; P=4.0×10(-6)). In a larger set of sequenced samples from Icelanders, we found another loss-of-function ASGR1 variant (p.W158X, carried by 1 in 1850 persons) that was also associated with lower levels of non-HDL cholesterol (P=1.8×10(-3)). CONCLUSIONS: ASGR1 haploinsufficiency was associated with reduced levels of non-HDL cholesterol and a reduced risk of coronary artery disease. (Funded by the National Institutes of Health and others.)

Storm activity in ancient climates:1. Sensitivity of severe storms to climate forcing factors on geologic timescales

Severe storms are important agents of sediment transport, and they generate sedimentary structures and textures that can be identified in the geologic record. The genesis and the distribution of storms are associated with distinctive meteorological controls, which in many cases lend themselves to analysis using general circulation models of the atmosphere. The goal of this study is to predict the distribution of severe storms in Earth history and to evaluate the correspondence between climate model predictions and geologic observations for widely different past climate conditions. The first step toward achieving this goal is an assessment of the importance of different climatic forcing factors, including paleogeography, topography, solar luminosity, carbon dioxide concentrations, and ocean heat transport variations. This assessment is based on sensitivity experiments using the GENESIS general circulation model. Paleogeography plays the most important role in governing the distribution of winter storms and plays a major role in hurricane genesis and steering. In contrast, changes in carbon dioxide, ocean heat transport, and solar luminosity exhibit little influence on the distribution of winter storms or the steering of hurricanes. However, these factors influence the strength of winter storms and the area and frequency of hurricane generation. The relationships between climatic forcing factors and storm genesis and distribution provide considerable guidance in comparisons of model predictions with observations of severe storms in Earth history and for the interpretations of storm deposits. The comparison of model predictions to the geologic record is the subject PSUCLIM 2 [this issue]

Storm activity in ancient climates 2. An analysis using climate simulations and sedimentary structures.

Severe storms generate sedimentary structures and textures that can be identified in the geologic record. A companion paper [PSUCLIM, this issue] describes the genesis and distribution of both winter storms and hurricanes and their sensitivity to climatic and geographic variables. In this paper, a total of 90 storm deposits are compared to GENESIS climate simulations in order to examine storm activity from the Permian to the Cretaceous and to evaluate the ability of the model to predict storms in ancient environments. Approximately 70% of the observed deposits are predicted by the models. The majority of the missed deposits are associated with recognizable errors. If these specific sources of error are eliminated, the model predicts over 90% of observed deposits. This degree of accuracy allows the assignment of generative processes to individual deposits; however, causative differences between hummocky cross stratification and tempestite type deposits are not distinguishable. The distribution of severe storms through Earth history varies as a function of both continental geometry and climate. Elevated atmospheric CO2 appears to homogenize the latitudinal distribution of storm deposits by expanding the area of hurricane genesis. Geography exerted the dominant control on winter storm distribution and was responsible for a shift in the concentration of winter storm deposits from the Southern Hemisphere in the Early Permian to the Northern Hemisphere in the mid-Cretaceous.Anna M. Agustsdottir, Eric J. Barron, Karen L. Bice, Lee A. Colarusso, Janette L. Cookman, Brian A. Cosgrove, Jennifer L. De Lurio, Jan F. Dutton, Brent J. Frakes, Lawrence A. Frakes, Carmen J. Moy, Thomas D. Olszewski, Richard D. Pancost, Christopher J. Poulsen, Charles M. Ruffner, Douglas G. Sheldon, and Timothy S. White

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Quantitative UPLC-MS/MS assay of urinary 2,8-dihydroxyadenine for diagnosis and management of adenine phosphoribosyltransferase deficiency.

To access publisher's full text version of this article click on the hyperlink at the bottom of the pageAdenine phosphoribosyltransferase (APRT) deficiency is a hereditary disorder that leads to excessive urinary excretion of 2,8-dihydroxyadenine (DHA), causing nephrolithiasis and chronic kidney disease. Treatment with allopurinol or febuxostat reduces DHA production and attenuates the renal manifestations. Assessment of DHA crystalluria by urine microscopy is used for therapeutic monitoring, but lacks sensitivity. We report a high-throughput assay based on ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) for quantification of urinary DHA. The UPLC-MS/MS assay was optimized by a chemometric approach for absolute quantification of DHA, utilizing isotopically labeled DHA as an internal standard. Experimental screening was conducted with D-optimal design and optimization of the DHA response was performed with central composite face design and related to the peak area of DHA using partial least square regression. Acceptable precision and accuracy of the DHA concentration were obtained over a calibration range of 100 to 5000ng/mL on three different days. The intra- and inter-day accuracy and precision coefficients of variation were well within ±15% for quality control samples analyzed in replicates of six at three concentration levels. Absolute quantification of DHA in urine samples from patients with APRT deficiency was achieved wihtin 6.5min. Measurement of DHA in 24h urine samples from three patients with APRT deficiency, diluted 1:15 (v/v) with 10mM ammonium hydroxide (NH4OH), yielded a concentration of 3021, 5860 and 10563ng/mL and 24h excretion of 816, 1327 and 1649mg, respectively. A rapid and robust UPLC-MS/MS assay for absolute quantification of DHA in urine was successfully developed. We believe this method will greatly facilitate diagnosis and management of patients with APRT deficiency.Rare Kidney Stone Consortium (U54DK083908), Rare Diseases Clinical Research Network (RDCRN), National Center for Advancing Translational Sciences (NCATS). National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK