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A catalog of genetic loci associated with kidney function from analyses of a million individuals
(2019)
Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through transancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these,147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m(2)/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m(2) at follow-up among those with eGFRcrea 60 mL/min/1.73m(2) or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or (LARP4B). Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
Rapid decline of glomerular filtration rate estimated from creatinine (eGFRcrea) is associated with severe clinical endpoints. In contrast to cross-sectionally assessed eGFRcrea, the genetic basis for rapid eGFRcrea decline is largely unknown. To help define this, we meta-analyzed 42 genome-wide association studies from the Chronic Kidney Diseases Genetics Consortium and United Kingdom Biobank to identify genetic loci for rapid eGFRcrea decline. Two definitions of eGFRcrea decline were used: 3 mL/min/1.73m(2)/year or more ("Rapid3"; encompassing 34,874 cases, 107,090 controls) and eGFRcrea decline 25% or more and eGFRcrea under 60 mL/min/1.73m(2) at follow-up among those with eGFRcrea 60 mL/min/1.73m(2) or more at baseline ("CKDi25"; encompassing 19,901 cases, 175,244 controls). Seven independent variants were identified across six loci for Rapid3 and/or CKDi25: consisting of five variants at four loci with genome-wide significance (near UMOD-PDILT (2), PRKAG2, WDR72, OR2S2) and two variants among 265 known eGFRcrea variants (near GATM, LARP4B). All these loci were novel for Rapid3 and/or CKDi25 and our bioinformatic follow-up prioritized variants and genes underneath these loci. The OR2S2 locus is novel for any eGFRcrea trait including interesting candidates. For the five genome-wide significant lead variants, we found supporting effects for annual change in blood urea nitrogen or cystatin-based eGFR, but not for GATM or (LARP4B). Individuals at high compared to those at low genetic risk (8-14 vs. 0-5 adverse alleles) had a 1.20-fold increased risk of acute kidney injury (95% confidence interval 1.08-1.33). Thus, our identified loci for rapid kidney function decline may help prioritize therapeutic targets and identify mechanisms and individuals at risk for sustained deterioration of kidney function.
By traversing the plume erupting from high southern latitudes on Saturn's moon Enceladus, Cassini orbiter instruments can directly sample the material therein. Cassini Plasma Spectrometer, CAPS, data show that a major plume component comprises previously-undetected particles of nanometer scales and larger that bridge the mass gap between previously observed gaseous species and solid icy grains. This population is electrically charged both negative and positive, indicating that subsurface triboelectric charging, i.e., contact electrification of condensed plume material may occur through mutual collisions within vents. The electric field of Saturn's magnetosphere controls the jets' morphologies, separating particles according to mass and charge. Fine-scale structuring of these particles' spatial distribution correlates with discrete plume jets' sources, and reveals locations of other possible active regions. The observed plume population likely forms a major component of high velocity nanometer particle streams detected outside Saturn's magnetosphere.
Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.
We present constraints on the mean dark energy density, Omega(X) and dark energy equation of state parameter, w(X), based on Chandra measurements of the X-ray gas mass fraction in 26 X-ray luminous, dynamically relaxed galaxy clusters spanning the redshift range 0.07 < z < 0.9. Under the assumption that the X-ray gas mass fraction measured within r(2500) is constant with redshift and using only weak priors on the Hubble constant and mean baryon density of the Universe, we obtain a clear detection of the effects of dark energy on the distances to the clusters, confirming (at comparable significance) previous results from Type la supernovae studies. For a standard Lambda cold dark matter (CDM) cosmology with the curvature Omega(K) included as a free parameter, we find Omega(Lambda) = 0.94(-0.23)(+0.21) (68 per cent confidence limits). We also examine extended XCDM dark energy models. Combining the Chandra data with independent constraints from cosmic microwave background experiments, we find Omega(X) = 0.75 +/- 0.04, Omega(m) = 0.26(- 0.04)(+0.06) and w(X) =-1.26 +/- 0.24. Imposing the prior constraint w(X) > -1, the same data require w(X) < -0.7 at 95 per cent confidence. Similar results on the mean matter density and dark energy equation of state parameter, &UOmega;(m) = 0.24 ± 0.04 and w(X) 1.20(-0.28)(+0.24), are obtained by replacing the cosmic microwave background data with standard priors on the Hubble constant and mean baryon density and assuming a flat geometry
We present an improved method for predicting the Sunyaev-Zeldovich (SZ) effect in galaxy clusters from spatially resolved, spectroscopic X-ray data. Using the deprojected electron density and temperature profiles measured within a fraction of the virial radius, and assuming a Navarro-Frenk-White mass model, we show how the pressure profile of the X-ray gas can be extrapolated to large radii, allowing the Comptonization parameter profile for the cluster to be predicted precisely. We apply our method to Chandra observations of three X-ray-luminous, dynamically relaxed clusters with published SZ data: RX J1347.5-1145, Abell 1835 and Abell 478. Combining the predicted and observed SZ signals, we determine improved estimates for the Hubble constant from each cluster and obtain a weighted mean of H (0) = 69 +/- 8 km s(-1) Mpc(-1) for a cosmology with Omega(m) = 0.3 and Omega(Lambda) = 0.7. This result is in good agreement with independent findings from the Hubble Key Project and the combination of cosmic microwave background and galaxy cluster data
We present a data set of images of the gravitationally lensed quasar Q2237+0305, that was obtained at the Apache Point Observatory (APO) between June 1995 and January 1998. Although the images were taken under variable, often poor seeing conditions and with coarse pixel sampling, photometry is possible for the two brighter quasar images A and B with the help of exact quasar image positions from HST observations. We obtain a light curve with 73 data points for each of the images A and B. There is evidence for a long (ga 100 day) brightness peak in image A in 1996 with an amplitude of about 0.4 to 0.5 mag (relative to 1995), which indicates that microlensing has been taking place in the lensing galaxy. Image B does not vary much over the course of the observation period. The long, smooth variation of the light curve is similar to the results from the OGLE monitoring of the system (Wozniak et al. cite{Wozniak00}). Based on observations obtained with the Apache Point Observatory 3.5-meter telescope, which is owned and operated by the Astrophysical Research Consortium.
Microlensing results from APO monitoring of the double quasar Q0957+561A,B between 1995 and 1998
(2000)
If the halo of the lensing galaxy 0957+561 is made of massive compact objects (MACHOs), they must affect the lightcurves of the quasar images Q0957+561 A and B differently. We search for this microlensing effect in the double quasar by comparing monitoring data for the two images A and B - obtained with the 3.5m Apache Point Observatory from 1995 to 1998 - with intensive numerical simulations. This way we test whether the halo of the lensing galaxy can be made of MACHOs of various masses. We can exclude a halo entirely made out of MACHOs with masses between 10-6 Msun and 10-2 Msun for quasar sizes of less than 3x 1014 h60-1/2 cm, hereby extending previous limits upwards by one order of magnitude.
In this thesis we use the gravitational lensing effect as a tool to tackle two rather different cosmological topics: the nature of the dark matter in galaxy halos, and the rotation of the universe. Firstly, we study the microlensing effect in the gravitational lens systems Q0957+561 and Q2237+0305. In these systems the light from the quasar shines directly through the lensing galaxy. Due to the relative motion of the quasar, the lensing galaxy, and the observer compact objects in the galaxy or galaxy halo cause brightness fluctuations of the light from the background quasar. We compare light curve data from a monitoring program of the double quasar Q0957+561 at the 3.5m telescope at Apache Point Observatory from 1995 to 1998 (Colley, Kundic & Turner 2000) with numerical simulations to test whether the halo of the lensing galaxy consists of massive compact objects (MACHOs). This test was first proposed by Gott (1981). We can exclude MACHO masses from 10^-6 M_sun up to 10^-2 M_sun for quasar sizes of less than 3x10^14 h_60^-0.5 cm if the MACHOs make up at least 50% of the dark halo. Secondly, we present new light curve data for the gravitationally lensed quadruple quasar Q2237+0305 taken at the 3.5m telescope at Apache Point Observatory from June 1995 to January 1998. Although the images were taken under variable, often poor seeing conditions and with coarse pixel sampling, photometry is possible for the two brighter quasar images A and B with the help from HST observations. We find independent evidence for a brightness peak in image A of 0.4 to 0.5 mag with a duration of at least 100 days, which indicates that microlensing has taken place in the lensing galaxy. Finally, we use the weak gravitational lensing effect to put limits on a class of Goedel-type rotating cosmologies described by Korotky & Obukhov (1996). In weak lensing studies the shapes of thousands of background galaxies are measured and averaged to reveal coherent gravitational distortions of the galaxy shapes by foreground matter distributions, or by the large-scale structure of space-time itself. We calculate the predicted shear as a function of redshift in Goedel-type rotating cosmologies and compare this to the upper limit on cosmic shear gamma_limit of approximately 0.04 from weak lensing studies. We find that Goedel-type models cannot have larger rotations omega than H_0=6.1x10^-11 h_60/year if this shear limit is valid for the whole sky.