A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling

<p>Abstract</p> <p>Background</p> <p>High-throughput DNA methylation arrays are likely to accelerate the pace of methylation biomarker discovery for a wide variety of diseases. A potential problem with a standard set of probes measuring the methylation status of CpG sites across the whole genome is that many sites may not show inter-individual methylation variation among the biosamples for the disease outcome being studied. Inclusion of these so-called "non-variable sites" will increase the risk of false discoveries and reduce statistical power to detect biologically relevant methylation markers.</p> <p>Results</p> <p>We propose a method to estimate the proportion of non-variable CpG sites and eliminate those sites from further analyses. Our method is illustrated using data obtained by hybridizing DNA extracted from the peripheral blood mononuclear cells of 311 samples to an array assaying 1505 CpG sites. Results showed that a large proportion of the CpG sites did not show inter-individual variation in methylation.</p> <p>Conclusions</p> <p>Our method resulted in a substantial improvement in association signals between methylation sites and outcome variables while controlling the false discovery rate at the same level.</p

Prenatal Famine and Genetic Variation Are Independently and Additively Associated with DNA Methylation at Regulatory Loci within IGF2/H19

Both the early environment and genetic variation may affect DNA methylation, which is one of the major molecular marks of the epigenome. The combined effect of these factors on a well-defined locus has not been studied to date. We evaluated the association of periconceptional exposure to the Dutch Famine of 1944–45, as an example of an early environmental exposure, and single nucleotide polymorphisms covering the genetic variation (tagging SNPs) with DNA methylation at the imprinted IGF2/H19 region, a model for an epigenetically regulated genomic region. DNA methylation was measured at five differentially methylated regions (DMRs) that regulate the imprinted status of the IGF2/H19 region. Small but consistent differences in DNA methylation were observed comparing 60 individuals with periconceptional famine exposure with unexposed same-sex siblings at all IGF2 DMRs (PBH<0.05 after adjustment for multiple testing), but not at the H19 DMR. IGF2 DMR0 methylation was associated with IGF2 SNP rs2239681 (PBH = 0.027) and INS promoter methylation with INS SNPs, including rs689, which tags the INS VNTR, suggesting a mechanism for the reported effect of the VNTR on INS expression (PBH = 3.4×10−3). Prenatal famine and genetic variation showed similar associations with IGF2/H19 methylation and their contributions were additive. They were small in absolute terms (<3%), but on average 0.5 standard deviations relative to the variation in the population. Our analyses suggest that environmental and genetic factors could have independent and additive similarly sized effects on DNA methylation at the same regulatory site

Open Data from the Third Observing Run of LIGO, Virgo, KAGRA, and GEO

The global network of gravitational-wave observatories now includes five detectors, namely LIGO Hanford, LIGO Livingston, Virgo, KAGRA, and GEO 600. These detectors collected data during their third observing run, O3, composed of three phases: O3a starting in 2019 April and lasting six months, O3b starting in 2019 November and lasting five months, and O3GK starting in 2020 April and lasting two weeks. In this paper we describe these data and various other science products that can be freely accessed through the Gravitational Wave Open Science Center at https://gwosc.org. The main data set, consisting of the gravitational-wave strain time series that contains the astrophysical signals, is released together with supporting data useful for their analysis and documentation, tutorials, as well as analysis software packages

Constraints on the Cosmic Expansion History from GWTC-3

We use 47 gravitational wave sources from the Third LIGO-Virgo-Kamioka Gravitational Wave Detector Gravitational Wave Transient Catalog (GWTC-3) to estimate the Hubble parameter H(z), including its current value, the Hubble constant H0. Each gravitational wave (GW) signal provides the luminosity distance to the source, and we estimate the corresponding redshift using two methods: the redshifted masses and a galaxy catalog. Using the binary black hole (BBH) redshifted masses, we simultaneously infer the source mass distribution and H(z). The source mass distribution displays a peak around 34Me, followed by a drop-off. Assuming this mass scale does not evolve with the redshift results in a H(z) measurement, yielding H0 = 68+12-8 km s-1 Mpc-1 (68% credible interval) when combined with the H0 measurement from GW170817 and its electromagnetic counterpart. This represents an improvement of 17% with respect to the H0 estimate from GWTC-1. The second method associates each GW event with its probable host galaxy in the catalog GLADE+, statistically marginalizing over the redshifts of each event's potential hosts. Assuming a fixed BBH population, we estimate a value of H0 = 68+8-6 km s-1 Mpc-1 with the galaxy catalog method, an improvement of 42% with respect to our GWTC-1 result and 20% with respect to recent H0 studies using GWTC-2 events. However, we show that this result is strongly impacted by assumptions about the BBH source mass distribution; the only event which is not strongly impacted by such assumptions (and is thus informative about H0) is the well-localized event GW190814

Changing Polygenic Penetrance on Phenotypes in the 20th Century Among Adults in the US Population

This study evaluates changes in genetic penetrance—defined as the association between an additive polygenic score and its associated phenotype—across birth cohorts. Situating our analysis within recent historical trends in the U.S., we show that, while height and BMI show increasing genotypic penetrance over the course of 20(th) Century, education and heart disease show declining genotypic effects. Meanwhile, we find genotypic penetrance to be historically stable with respect to depression. Our findings help inform our understanding of how the genetic and environmental landscape of American society has changed over the past century, and have implications for research which models gene-environment (GxE) interactions, as well as polygenic score calculations in consortia studies that include multiple birth cohorts

The effect of different design concepts in lumbar total disc arthroplasty on the range of motion, facet joint forces and instantaneous center of rotation of a L4-5 segment

Although both unconstrained and constrained core lumbar artificial disc designs are in clinical use, the effect of their design on the range of motion, center of rotations, and facet joint forces is not well understood. It is assumed that the constrained configuration causes a fixed center of rotation with high facet forces, while the unconstrained configuration leads to a moving center of rotation with lower loaded facets. The authors disagree with both assumptions and hypothesized that the two different designs do not lead to substantial differences in the results. For the different implant designs, a three-dimensional finite element model was created and subsequently inserted into a validated model of a L4-5 lumbar spinal segment. The unconstrained design was represented by two implants, the Charité® disc and a newly developed disc prosthesis: Slide-Disc®. The constrained design was obtained by a modification of the Slide-Disc® whereby the inner core was rigidly connected to the lower metallic endplate. The models were exposed to an axial compression preload of 1,000 N. Pure unconstrained moments of 7.5 Nm were subsequently applied to the three anatomical main planes. Except for extension, the models predicted only small and moderate inter-implant differences. The calculated values were close to those of the intact segment. For extension, a large difference of about 45% was calculated between both Slide-Disc designs and the Charité® disc. The models predicted higher facet forces for the implants with an unconstrained core compared to an implant with a constrained core. All implants caused a moving center of rotation. Except for axial rotation, the unconstrained and constrained configurations mimicked the intact situation. In axial rotation, only the Slide-Disc® with mobile core reproduced the intact behavior. Results partially support our hypothesis and imply that different implant designs do not lead to strong differences in the range of motion and the location of center of rotations. In contrast, facet forces appeared to be strongly dependent on the implant design. However, due to the great variability in facet forces reported in the literature, together with our results, we could speculate that these forces may be more dependent on the individual spine geometry rather than a specific implant design