Andrew D. Paterson

The paper assesses Hardy-Weinberg equilibrium deviations in whole genome sequence data from the 1000 Genomes Project, identifying SNPs with technical rather than biological deviations.

The paper develops a statistical framework for Hardy-Weinberg equilibrium testing on the X chromosome, showing that existing methods can have inflated type I error or misleading results when sex differences in minor allele frequency are present.

The paper introduces DRLPC to reduce multi-collinearity in SNP data, improving regression analysis power in two datasets.

The paper uses proteogenomic data to identify circulating proteins associated with type 1 diabetes risk and explores their tissue-specific expression.

RegionScan provides an R package for region-level genome-wide association testing and visualization, supporting multiple-variant and single-variant hypothesis testing with LD-adaptive region definition.

The paper identifies variance quantitative trait loci (vQTLs) for vitamin D levels and characterizes gene-environment interactions involving modifiable factors and sex.

This paper introduces a method to indirectly test gene-environment interactions for binary traits by leveraging non-additive genetic effects and applies it to the UK Biobank dataset.

The paper shows that penetrance estimates for rare variants can be unreliable due to ascertainment bias and introduces PenEst, an app to analyze this effect, along with LOD score corrections for pathogenicity assessment.

This paper develops a joint model to identify direct and indirect genetic associations of SNPs with time-to-event traits in longitudinal studies, demonstrating improved accuracy in disease progression analysis.

This study performs sex-stratified GWAS of body fat percentage in the UK Biobank, adjusting for testosterone and SHBG, and identifies new loci with limited genetic overlap between males and females.

The paper re-evaluates the inclusion of sex chromosomes in GWAS, finding persistent underrepresentation and proposing recommendations for improvement.

The paper identifies significant sex differences in minor allele frequencies for X chromosome variants in the 1000 Genomes Project data, highlighting the need to account for these differences in future analyses.

This paper compares two genome-wide association studies on heart rate response to exercise from the UK Biobank, finding common SNPs and PRS agreement but differences due to trait definitions and analytic approaches.

This study identifies a genome-wide significant variant for OC traits and shows shared genetic risk between OC traits and OCD.

This paper assesses the statistical power of case-control genomic studies for identifying host genetic factors associated with COVID-19 susceptibility and severity using simulations and current epidemiological estimates.

This study identifies a 4bp non-coding deletion in the FOXG1 locus at 14q12 as a candidate for isolated strabismus, showing its potential role in regulating FOXG1 expression.

The paper compares data integration methods in GWAS using functional annotations, finding that weighted p-value methods identify more variants than sFDR, though sFDR is more robust to uninformative scores.

TRUFFLE detects IBD segments and estimates relatedness in un-phased genetic data efficiently and accurately, outperforming existing methods in speed and reducing false positives.

This study identifies 16 genome-wide significant loci associated with diabetic kidney disease, including a protective variant in the COL4A3 gene.