A5065532777- Genetic Associations and Epidemiology
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Nutrition, Genetics, and Disease
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Cell Image Analysis Techniques
- Genetic Syndromes and Imprinting
- Alcohol Consumption and Health Effects
- Advanced Fluorescence Microscopy Techniques
- Liver Disease Diagnosis and Treatment
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Retinal Diseases and Treatments
- Vitamin C and Antioxidants Research
- Gene Regulatory Network Analysis
- Evolution and Genetic Dynamics
- Health and Medical Studies
- Endoplasmic Reticulum Stress and Disease
- CRISPR and Genetic Engineering
- Lipid metabolism and disorders
- Genomic variations and chromosomal abnormalities
- Autoimmune Bullous Skin Diseases
- Retinopathy of Prematurity Studies
New York Genome Center
2022-2025
The University of Queensland
2018-2024
New York Proton Center
2024
Westlake University
2022-2023
Imperial College London
2017-2023
Genomics England
2017
Guangzhou Blood Center
2017
To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects European ancestry after imputation using 1000 Genomes multiethnic reference panel. Promising signals were followed up in additional sets (of 14,545 or 7,397 38,994 71,604 subjects). We identified 13 novel T2D-associated loci (P < 5 × 10-8), including variants near GLP2R, GIP, HLA-DQA1...
Abstract Understanding how natural selection has shaped genetic architecture of complex traits is importance in medical and evolutionary genetics. Bayesian methods have been developed using individual-level GWAS data to estimate multiple parameters including signature. Here, we present a method (SBayesS) that only requires summary statistics. We analyse for 155 (n = 27k–547k) project the estimates onto those obtained from simulations. that, on average across traits, about 1% human genome...
Abstract A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior pooling. We introduce scSplit utilizes genetic differences inferred from scRNA-seq data alone samples. also enables mapping clusters original Using simulated, merged, and multi-individual datasets, we show that prediction is highly concordant with demuxlet predictions consistent the known truth...
Abstract Genome-wide association studies (GWAS) have discovered numerous genetic variants associated with human behavioural traits. However, traits are subject to misreports and longitudinal changes (MLC) which can cause biases in GWAS follow-up analyses. Here, we demonstrate that individuals higher disease burden the UK Biobank ( n = 455,607) more likely misreport or reduce their alcohol consumption levels, propose a correction procedure mitigate MLC-induced biases. The signals removed by...
ABSTRACT Recent advancements in functional genomics have provided an unprecedented ability to measure diverse molecular modalities, but learning causal regulatory relationships from observational data remains challenging. Here, we leverage pooled genetic screens and single cell sequencing (i.e. Perturb-seq) systematically identify the targets of signaling regulators biological contexts. We demonstrate how Perturb-seq is compatible with recent commercially available advances combinatorial...
Abstract Background Substance use behaviours (SUB) including smoking, alcohol consumption, and coffee intake are associated with many health outcomes. However, whether the effects of SUB causal remains controversial, especially for consumption intake. Methods In this study, we assess 11 commonly used Mendelian Randomization (MR) methods by simulation apply them to investigate relationship between 7 traits We also combine stratified regression, genetic correlation, MR analyses...
Abstract Genome-wide association studies (GWAS) in samples of European ancestry have identified thousands genetic variants associated with complex traits humans. However, it remains largely unclear whether these associations can be used non-European populations. Here, we seek to quantify the proportion variation for a trait shared between continental We estimated between-population correlation effects at all SNPs ( $$r_{g}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">...
ABSTRACT The genome-wide association study (GWAS) has been widely used as an experimental design to detect associations between genetic variants and a phenotype. Two major confounding factors, population stratification relatedness, could potentially lead inflated GWAS test-statistics thereby spurious associations. Mixed linear model (MLM)-based approaches can be account for sample structure. However, (GWA) analyses in biobank samples such the UK Biobank (UKB) often exceed capability of most...
Abstract We assessed the reproducibility of differentially expressed genes (DEGs) in previously published Alzheimer’s (AD), Parkinson’s (PD), Schizophrenia (SCZ), and COVID-19 scRNA-seq studies. While transcriptional scores from DEGs individual PD datasets had moderate predictive power for case-control status other (AUC=0.77 0.75), AD SCZ poor (AUC=0.68 0.55). developed a non-parametric meta-analysis method, SumRank, based on relative differential expression ranks across datasets, found with...
Abstract Understanding the difference in genetic regulation of gene expression between brain and blood is important for discovering genes associated with brain-related traits disorders. Here, we estimate correlation effects at top cis -expression (cis-eQTLs or cis-mQTLs) expressed (or CpG sites methylated) both tissues, while accounting errors their estimated ( r b ). Using publicly available data n = 72 to l,366), find that cis-eQTLs P eQTL < 5×10 −8 ) mQTLs mQTL 1×10 −10 are highly...
Abstract Understanding how natural selection has shaped the genetic architecture of complex traits and diseases is importance in medical evolutionary genetics. Bayesian methods have been developed using individual-level data to estimate multiple features architecture, including signatures selection. Here, we present an enhanced method (SBayesS) that only requires GWAS summary statistics incorporates functional genomic annotations. We analysed with large sample sizes for 155 detected...
Abstract Homeostatic control of blood glucose requires different physiological responses in the fasting and post-prandial states. We reasoned that measurements under non-standardised conditions (random glucose; RG) may capture diverse glucoregulatory processes more effectively than previous genome-wide association studies (GWAS) glycaemia or after standardised loads. Through GWAS meta-analysis RG 493,036 individuals without diabetes ethnicities we identified 128 associated loci represented...
Abstract Gene-based association tests aggregate multiple SNP-trait associations into sets defined by gene boundaries. Since genes have a direct biological link to downstream function, gene-based test results are widely used in post-GWAS analysis. A common approach for is combine SNPs computing the sum of χ 2 statistics. However, this strategy ignores directions SNP effects, which could result loss power with masking effects (e.g., when product two and their linkage disequilibrium (LD)...