The paper develops a variance prioritisation method to detect gene-interaction effects on blood biomarker concentrations using UK Biobank data, identifying novel gene-environment and gene-gene interactions.

medRxiv · Jan 5, 2022 · PreprintGenetic & Genomic Medicine

A robust mean and variance test with application tohigh-dimensional phenotypes

James R Staley, Frank A. G. Windmeijer, Matthew J Suderman, Matthew Lyon, George Davey Smith, Kate M. Tilling

The paper introduces a robust statistical test for detecting associations with both mean and variability in high-dimensional phenotypes, applied to DNA methylation data.

European Journal of Epidemiology · Oct 15, 2021Peer-reviewedBioinformatics

Genetic effect modification of cis-acting C-reactive protein variants in cardiometabolic disease status

Jie Zheng, Haotian Tang, Matthew Lyon, Neil M Davies, Venexia M. Walker, James S. Floyd, Thomas R. Austin, Ali Shojaie, Bruce M. Psaty, Tom R. Gaunt, George Davey Smith

This study shows genetic associations of CRP variants with BMI differ between individuals with and without cardiometabolic diseases, suggesting BMI modifies these genetic effects.

bioRxiv · Sep 23, 2021 · PreprintGenetics

The variant call format provides efficient and robust storage of GWAS summary statistics

Matthew Lyon, Shea J. Andrews, Benjamin Elsworth, Tom R. Gaunt, Gibran Hemani, Edoardo M. Marcora

The paper introduces GWAS-VCF, a variant call format for GWAS summary statistics, showing it is faster and more robust than tabular formats for data extraction and analysis.

Genome biology · Jan 13, 2021Peer-reviewedGenetics

EpiGraphDB: a database and data mining platform for health data science

Yi Liu, Benjamin Elsworth, Pau Erola, Valeriia Haberland, Gibran Hemani, Matthew Lyon, Jie Zheng, Oliver C Lloyd, Marina Vabistsevits, Tom R. Gaunt

EpiGraphDB is a graph database and analytical platform for health data science, demonstrating its utility through case studies on pleiotropy, drug targets, and causal inference.

Bioinformatics · Nov 4, 2020Peer-reviewedBioinformatics

The MRC IEU OpenGWAS data infrastructure

Benjamin Elsworth, Matthew Lyon, Tessa Alexander, Yi Liu, Peter Matthews, Jon Hallett, Phil Bates, Tom Palmer, Valeriia Haberland, George Davey Smith, Jie Zheng, Philip Haycock, Tom R. Gaunt, Gibran Hemani

OpenGWAS serves 14582 harmonised, complete GWAS summary datasets (125.8 billion associations) via API, R/Python clients and GWAS-VCF downloads, with glue code for Mendelian randomization, colocalisation and fine-mapping.

bioRxiv · Aug 10, 2020 · PreprintGenetics✦ In-depth digest