A method to estimate the contribution of rare coding variants to complex trait heritability.

It has been postulated that rare coding variants (RVs; MAF < 0.01) contribute to the "missing" heritability of complex traits. We developed a framework, the Rare variant heritability (RARity) estimator, to assess RV heritability (h) without assuming a particular genetic architecture.

B-Type Fumonisins in Post-Fermented Tea: Occurrence and Consumer Dietary Exposure in Guangxi, China.

Post-fermented tea (PFT), a commonly consumed beverage worldwide, is characterized by the rapid growth of its microbial groups and the substantial changes they undergo. Consequently, PFT may contain mycotoxins such as B-type fumonisins (FBs). This study aimed to assess the intake of FBs through the consumption of PFT among consumers in Guangxi, China.

Surrogate Adiposity Markers and Mortality.

Importance: Body mass index (BMI) is an easily obtained adiposity surrogate. However, there is variability in body composition and adipose tissue distribution between individuals with the same BMI, and there is controversy regarding the BMI associated with the lowest mortality risk.

Objective: To evaluate which of BMI, fat mass index (FMI), and waist-to-hip (WHR) has the strongest and most consistent association with mortality.

A versatile, fast and unbiased method for estimation of gene-by-environment interaction effects on biobank-scale datasets.

Identification of gene-by-environment interactions (GxE) is crucial to understand the interplay of environmental effects on complex traits. However, current methods evaluating GxE on biobank-scale datasets have limitations. We introduce MonsterLM, a multiple linear regression method that does not rely on model specification and provides unbiased estimates of variance explained by GxE.

Cost-Effectiveness of Polygenic Risk Scores to Guide Statin Therapy for Cardiovascular Disease Prevention.

Background: Atherosclerotic cardiovascular diseases (CVDs) are leading causes of death despite effective therapies and result in unnecessary morbidity and mortality throughout the world. We aimed to investigate the cost-effectiveness of polygenic risk scores (PRS) to guide statin therapy for Canadians with intermediate CVD risk and model its economic outlook.

Methods: This cost-utility analysis was conducted using UK Biobank prospective cohort study participants, with recruitment from 2006 to 2010, and at least 10 years of follow-up.

Fine-tuning of Genome-Wide Polygenic Risk Scores and Prediction of Gestational Diabetes in South Asian Women.

Gestational diabetes Mellitus (GDM) affects 1 in 7 births and is associated with numerous adverse health outcomes for both mother and child. GDM is suspected to share a large common genetic background with type 2 diabetes (T2D). The aim of our study was to characterize different GDM polygenic risk scores (PRSs) and test their association with GDM using data from the South Asian Birth Cohort (START).

Effects of withering on the main physical properties of withered tea leaves and the sensory quality of congou black tea.

To explore the relationship between the moisture content of withered tea leaves and their physical properties (i.e., elasticity, plasticity, flexibility, and texture) during withering, texture analyzer was employed to test the elasticity and flexibility of withered tea leaves with different moisture contents.

Author Correction: A machine-learning heuristic to improve gene score prediction of polygenic traits.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Analytical strategies to include the X-chromosome in variance heterogeneity analyses: Evidence for trait-specific polygenic variance structure.

Genotype-stratified variance of a quantitative trait could differ in the presence of gene-gene or gene-environment interactions. Genetic markers associated with phenotypic variance are thus considered promising candidates for follow-up interaction or joint location-scale analyses. However, as in studies of main effects, the X-chromosome is routinely excluded from "whole-genome" scans due to analytical challenges.

Identification of Novel Causal Blood Biomarkers Linking Metabolically Favorable Adiposity With Type 2 Diabetes Risk.

Objective: Observations of a metabolically unhealthy normal weight phenotype suggest that a lack of favorable adiposity contributes to an increased risk of type 2 diabetes. We aimed to identify causal blood biomarkers linking favorable adiposity with type 2 diabetes risk for use in cardiometabolic risk assessments.

Research Design And Methods: A weighted polygenic risk score (PRS) underpinning metabolically favorable adiposity was validated in the UK Biobank ( = 341,872) and the Outcome Reduction With Initial Glargine Intervention (ORIGIN Trial) ( = 8,197) and tested for association with 238 blood biomarkers.

A robust method to estimate regional polygenic correlation under misspecified linkage disequilibrium structure.

Complex traits can share a substantial proportion of their polygenic heritability. However, genome-wide polygenic correlations between pairs of traits can mask heterogeneity in their shared polygenic effects across loci. We propose a novel method (weighted maximum likelihood-regional polygenic correlation [RPC]) to evaluate polygenic correlation between two complex traits in small genomic regions using summary association statistics.

Identification of key aromatic compounds in Congou black tea by partial least-square regression with variable importance of projection scores and gas chromatography-mass spectrometry/gas chromatography-olfactometry.

Background: Gas chromatography-olfactometry (GC-O) is the most frequently used method to estimate the sensory contribution of single odorant, but disregards the interactions between volatiles. In order to select the key volatiles responsible for the aroma attributes of Congou black tea (Camellia sinensis), instrumental, sensory and multivariate statistical approaches were applied.

Results: Using sensory analysis, nine panellists developed eight descriptors: floral, sweet, fruity, green, roasted, oil, spicy, and off-odour.

A machine-learning heuristic to improve gene score prediction of polygenic traits.

Machine-learning techniques have helped solve a broad range of prediction problems, yet are not widely used to build polygenic risk scores for the prediction of complex traits. We propose a novel heuristic based on machine-learning techniques (GraBLD) to boost the predictive performance of polygenic risk scores. Gradient boosted regression trees were first used to optimize the weights of SNPs included in the score, followed by a novel regional adjustment for linkage disequilibrium.

A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics.

Despite considerable efforts, known genetic associations only explain a small fraction of predicted heritability. Regional associations combine information from multiple contiguous genetic variants and can improve variance explained at established association loci. However, regional associations are not easily amenable to estimation using summary association statistics because of sensitivity to linkage disequilibrium (LD).

A comparison of sperm RNA-seq methods.

A significant challenge to the effective application of RNA-seq to the complete transcript analysis of low quantity and/or degraded samples is the amplification of minimal input RNA to enable sequencing library construction. Several strategies have been commercialized in order to facilitate this goal. However, each strategy has its own specific protocols and methodology, and each may introduce unique bias and in some cases show specific preference for a collection of sequences.

Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling.

Different semen storage and sperm purification methods may affect the integrity of isolated spermatozoal RNA. RNA-Seq was applied to determine whether semen storage methods (pelleted vs. liquefied) and somatic cell lysis buffer (SCLB) vs.

Next-generation sequencing: a powerful tool for the discovery of molecular markers in breast ductal carcinoma in situ.

Mammographic screening leads to frequent biopsies and concomitant overdiagnosis of breast cancer, particularly ductal carcinoma in situ (DCIS). Some DCIS lesions rapidly progress to invasive carcinoma, whereas others remain indolent. Because we cannot yet predict which lesions will not progress, all DCIS is regarded as malignant, and many women are overtreated.

Stability, delivery and functions of human sperm RNAs at fertilization.

Increasing attention has focused on the significance of RNA in sperm, in light of its contribution to the birth and long-term health of a child, role in sperm function and diagnostic potential. As the composition of sperm RNA is in flux, assigning specific roles to individual RNAs presents a significant challenge. For the first time RNA-seq was used to characterize the population of coding and non-coding transcripts in human sperm.

RNA-Seq of human breast ductal carcinoma in situ models reveals aldehyde dehydrogenase isoform 5A1 as a novel potential target.

Breast ductal carcinoma in situ (DCIS) is being found in great numbers of women due to the widespread use of mammography. To increase knowledge of DCIS, we determined the expression changes that are common among three DCIS models (MCF10.DCIS, SUM102 and SUM225) compared to the MCF10A model of non-tumorigenic mammary epithelial cells in three dimensional (3D) overlay culture with reconstituted basement membrane (rBM).

Identification of artifactual microarray probe signals constantly present in multiple sample types.

The detection, identification, and quantitation of transcripts have evolved from simple Northern analysis, cDNA cloning, and sequencing to RT-PCR, microarrays, and now digital gene expression using ultra-high-throughput RNA sequencing (RNA-Seq). During the course of our studies we observed that some microarray probes show very high signal intensity values yet are discordant when compared with RNA-Seq. A total of 99 probes from approximately 30,000 were identified as consistently discordant in four human tissues or cell lines.

Transcriptional differences between rhesus embryonic stem cells generated from in vitro and in vivo derived embryos.

Numerous studies have focused on the transcriptional signatures that underlie the maintenance of embryonic stem cell (ESC) pluripotency. However, it remains unclear whether ESC retain transcriptional aberrations seen in in vitro cultured embryos. Here we report the first global transcriptional profile comparison between ESC generated from either in vitro cultured or in vivo derived primate embryos by microarray analysis.

Molecular and functional expression of cation-chloride cotransporters in dorsal root ganglion neurons during postnatal maturation.

GABA depolarizes and excites central neurons during early development, becoming inhibitory and hyperpolarizing with maturation. This "developmental shift" occurs abruptly, reflecting a decrease in intracellular Cl(-) concentration ([Cl(-)](i)) and a hyperpolarizing shift in Cl(-) equilibrium potential due to upregulation of the K(+)-Cl(-) cotransporter KCC2b, a neuron-specific Cl(-) extruder. In contrast, primary afferent neurons (PANs) are depolarized by GABA throughout adulthood because of expression of NKCC1, a Na(+)-K(+)-2Cl(-) cotransporter that accumulates Cl(-) above equilibrium.

A platform for evaluating sperm RNA biomarkers: dysplasia of the fibrous sheath--testing the concept.

Objective: To investigate the potential use of correlative microarray-based transcript pairs as candidate markers for male fertility using dysplasia of the fibrous sheath (DFS) as an affected model. It is widely recognized that microarray technology may be limited by cost and that the quality of the transcript remains relatively unknown. To address these issues, we analyzed the stable transcript pairs by qPCR with a systematic primer design process.

CTCF binds to sites in the major histocompatibility complex that are rapidly reconfigured in response to interferon-gamma.

Activation of the major histocompatibility complex (MHC) by interferon-gamma (IFN-γ) is a fundamental step in the adaptive immune response to pathogens. Here, we show that reorganization of chromatin loop domains in the MHC is evident within the first 30 min of IFN-γ treatment of fibroblasts, and that further dynamic alterations occur up to 6 h. These very rapid changes occur at genomic sites which are occupied by CTCF and are close to IFN-γ-inducible MHC genes.

Evaluation of inter-laboratory and cross-platform concordance of DNA microarrays through discriminating genes and classifier transferability.

Microarray technology has great potential for improving our understanding of biological processes, medical conditions, and diseases. Often, microarray datasets are collected using different microarray platforms (provided by different companies) under different conditions in different laboratories. The cross-platform and cross-laboratory concordance of the microarray technology needs to be evaluated before it can be successfully and reliably applied in biological/clinical practice.