Fast genomic μChIP-chip from 1,000 cells

A new method for rapid genome-wide μChIP-chip from as few as 1,000 cells

A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits.

Understanding the contribution of gene-environment interactions (GxE) to complex trait variation can provide insights into disease mechanisms, explain sources of heritability, and improve genetic risk prediction. While large biobanks with genetic and deep phenotypic data hold promise for obtaining novel insights into GxE, our understanding of GxE architecture in complex traits remains limited. We introduce a method to estimate the proportion of trait variance explained by GxE (GxE heritability) and additive genetic effects (additive heritability) across the genome and within specific genomic annotations. We show that our method is accurate in simulations and computationally efficient for biobank-scale datasets. We applied our method to common array SNPs (MAF ≥1%), fifty quantitative traits, and four environmental variables (smoking, sex, age, and statin usage) in unrelated white British individuals in the UK Biobank. We found 68 trait-E pairs with significant genome-wide GxE heritability (p<0.05/200) with a ratio of GxE to additive heritability of ≈6.8% on average. Analyzing ≈8 million imputed SNPs (MAF ≥0.1%), we documented an approximate 28% increase in genome-wide GxE heritability compared to array SNPs. We partitioned GxE heritability across minor allele frequency (MAF) and local linkage disequilibrium (LD) values, revealing that, like additive allelic effects, GxE allelic effects tend to increase with decreasing MAF and LD. Analyzing GxE heritability near genes highly expressed in specific tissues, we find significant brain-specific enrichment for body mass index (BMI) and basal metabolic rate in the context of smoking and adipose-specific enrichment for waist-hip ratio (WHR) in the context of sex

Endoscopic Posterior Cricoid Split with Costal Cartilage Graft: A Fifteen‐Year Experience

Objective To evaluate outcomes of the endoscopic posterior cricoid split with rib graft (EPCS/RG) procedure in the treatment of subglottic stenosis (SGS), posterior glottic stenosis (PGS), and bilateral vocal fold immobility (BVFI). Study Design Retrospective chart review. Methods Chart review of all patients who underwent EPCS/RG at a single tertiary-care facility between 1999 and 2014. Patients were grouped based on the primary indication for the procedure. Decannulation was the primary endpoint. Secondary endpoints were the number of subsequent airway procedures and length of hospitalization. Results Thirty-three patients were identified; 32 had tracheotomy. Overall decannulation rate was 65.6%. Subgroup analysis demonstrated the following decannulation rates: 53.8% for SGS, 100% for PGS, and 28.6% for BVFI. Fisher exact test found a significant difference in overall decannulation rates between groups (P = 0.002). Operation-specific decannulation rates for patients who never required an open procedure were 23% for SGS, 91.6% for PGS, and 28.6% for BVFI. This difference was also statistically significant (P = 0.001). Multivariate logistic regression analysis found prematurity had a positive correlation with decannulation that approached statistical significance (P < 0.051; odds ratio 6.1; 95% confidence interval 0.99, 37.6). The percentage of patients who underwent repeat airway procedures for the groups was 61.5% for SGS, 16.6 % for PGS, and 14.3% for BVFI. The median length of hospitalization after EPCS/RG was 3 days. Conclusion This represents the largest series of patients who have undergone EPCS/RG and demonstrates that the majority of patients can be decannulated after this procedure. Patients with PGS had the highest operation-specific decannulation rates

Histone H3 Lysine 27 Methylation Asymmetry on Developmentally-Regulated Promoters Distinguish the First Two Lineages in Mouse Preimplantation Embryos

First lineage specification in the mammalian embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to embryonic and extraembryonic tissues. We show here that this first differentiation event is accompanied by asymmetric distribution of trimethylated histone H3 lysine 27 (H3K27me3) on promoters of signaling and developmentally-regulated genes in the mouse ICM and TE. A genome-wide survey of promoter occupancy by H3K4me3 and H3K27me3 indicates that both compartments harbor promoters enriched in either modification, and promoters co-enriched in trimethylated H3K4 and H3K27 linked to developmental and signaling functions. The majority of H3K4/K27me3 co-enriched promoters are distinct between the two lineages, primarily due to differences in the distribution of H3K27me3. Derivation of embryonic stem cells leads to significant losses and gains of H3K4/K27me3 co-enriched promoters relative to the ICM, with distinct contributions of (de)methylation events on K4 and K27. Our results show histone trimethylation asymmetry on promoters in the first two developmental lineages, and highlight an epigenetic skewing associated with embryonic stem cell derivation

Statistical properties of simple random-effects models for genetic heritability

Abstract: Random-effects models are a popular tool for analysing total narrow-sense her-itability for simple quantitative phenotypes on the basis of large-scale SNP data. Recently, there have been disputes over the validity of conclusions that may be drawn from such analysis. We derive some of the fundamental statistical properties of heritability estimates arising from these models, showing that the bias will generally be small. We show that that the score function may be manipulated into a form that facilitates intelligible interpretations of the results. We use this score function to explore the behavior of the model when certain key assumptions of the model are not satisfied — shared environment, measurement error, and genetic effects that are confined to a small subset of sites — as well as to elucidate the meaning of negative heritability estimates that may arise. The variance and bias depend crucially on the variance of certain functionals of the singular values of the genotype matrix. A useful baseline is the singular value distribution associated with genotypes that are completely independent — that is, with no linkage and no relatedness— for a given number of individuals and sites. We calculate the corresponding variance and bias for this setting

A randomised comparison of a four- and a five-point scale version of the Norwegian Function Assessment Scale

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Molybdenum evidence for expansive sulfidic water masses in ~750Ma oceans

The Ediacaran appearance of large animals, including motile bilaterians, is commonly hypothesized to reflect a physiologically enabling increase in atmospheric and oceanic oxygen abundances (pO2). To date, direct evidence for low oxygen in pre-Ediacaran oceans has focused on chemical signatures in the rock record that reflect conditions in local basins, but this approach is both biased to constrain only shallower basins and statistically limited when we seek to follow the evolution of mean ocean chemical state through time. Because the abundance and isotopic composition of molybdenum (Mo) in organic-rich euxinic sediments can vary in response to changes in global redox conditions, Mo geochemistry provides independent constraints on the global evolution of well-oxygenated environments. Here, we establish a theoretical framework to access global marine Mo cycle in the past from the abundance and isotope composition of ancient seawater. Further, we investigate the ~ 750 Ma Walcott Member of the Chuar Group, Grand Canyon, which accumulated in a rift basin with open connection to the ocean. Iron speciation data from upper Walcott shales indicate that local bottom waters were anoxic and sulfidic, consistent with their high organic content (up to 20 wt.%). Similar facies in Phanerozoic successions contain high concentrations of redox-sensitive metals, but in the Walcott Member, abundances of Mo and U, as well as Mo/TOC (~ 0.5 ppm/wt.%) are low. δ98Mo values also fall well below modern equivalents (0.99 ± 0.13‰ versus ~ 2.35‰ today). These signatures are consistent with model predictions where sulfidic waters cover ~ 1–4% of the global seafloor, corresponding to a ~ 20–80 fold increase compared to the modern ocean. Therefore, our results suggest globally expansive sulfidic water masses in mid-Neoproterozoic oceans, bridging a nearly 700 million-year gap in previous Mo data. We propose that anoxic and sulfidic (euxinic) conditions governed Mo cycling in the oceans even as ferruginous subsurface waters re-appeared 800–750 Ma, and we interpret this anoxic ocean state to reflect a markedly lower atmospheric and oceanic O2 level, consistent with the hypothesis that pO2 acted as an evolutionary barrier to the emergence of large motile bilaterian animals prior to the Ediacaran Period.Organismic and Evolutionary Biolog