Jeffrey G. Reid

This study quantifies cancer risk and penetrance in CHEK2 heterozygotes using genomic data from two large biobanks, finding increased risks for several cancers and younger age of onset.

The paper improves rare variant association studies by using proteomics-informed large language models, identifying more gene-trait associations than existing methods.

The paper compares the effectiveness of whole genome sequencing, whole exome sequencing with imputation, and array genotyping in detecting genetic associations across 100 complex traits in the UK Biobank, finding that WES+IMP provides similar signal yield to WGS with greater efficiency.

The paper identifies a NOTCH3 variant, p.Arg1231Cys, enriched in South Asians and strongly associated with stroke risk, highlighting the importance of genetic diversity in stroke research.

This paper presents the largest catalog of human protein-coding variation from 985,830 individuals, identifying rare variants and their functional implications for precision medicine.

The paper genotypes and sequences 140,000 adults from the Mexico City Prospective Study, revealing ancestry diversity and developing imputation resources for genetic studies.

This study identifies 53 genetic loci associated with hearing loss, including 15 novel ones, using genome-wide and exome-sequencing data from multiple cohorts.

The paper examines genetic variation and natural selection at SARS-CoV-2 host genes in diverse populations and links selected variants to clinical phenotypes in COVID-19.

The paper identifies a rare variant that lowers ACE2 expression and reduces COVID-19 risk, and develops a genetic risk score predicting severe disease.

The paper identifies 51 known and 23 novel gene-disease associations using exome sequencing data from 200,000 UK Biobank participants, highlighting high-impact rare variants for 26 diseases and traits.

This study uses exome sequencing of 628,388 individuals to identify genetic variants associated with clonal hematopoiesis and its health outcomes.

This study evaluates polygenic risk scores (PRS) for cancer prediction in a racially diverse biobank, finding moderate improvements in discriminatory accuracy for European ancestry but limited gains for African ancestry.

This study identifies a rare variant in SLC30A10 associated with elevated ALT/AST and hypermanganesemia symptoms, suggesting broader health impacts beyond diagnosed cases.

The paper describes exome sequencing of 200,643 UK Biobank participants, providing a rich resource of coding variants for genetic and drug discovery research.

The paper introduces REGENIE, a fast whole genome regression method for quantitative and binary traits, showing computational efficiency and accuracy on UK Biobank data.

The paper identifies recessive NOD2 inheritance as a major driver of early onset Crohn’s Disease in both pediatric and adult cohorts.

In 159,701 siblings from 17 cohorts, population GWAS overstate direct effects on height, education, smoking, cognition, depressive symptoms and age at first birth; clinical traits mostly agree across models.

This study identifies robust gene-phenotype associations by analyzing rare loss-of-function variants in exome-wide data linked to electronic health records.

The paper defines an open-source, lossless read-mapping protocol for NGS data and demonstrates direct variant calling without base quality score recalibration.

The paper introduces spVCF, a compressed variant call format that reduces file size by over 10X with minimal information loss.

The paper validates gene-phenotype associations by mapping genes to ICD codes using UMLS relationships, finding 249,764 gene-ICD mappings in a cohort of 92,455 samples.

Multi-ethnic type 2 diabetes (T2D) meta-analysis of 228,499 cases and 1,178,783 controls finds 318 previously unreported loci, 804 expression-colocalized genes, and 13 SNP-by-T2D vascular-outcome interactions.

Exomes of 49,960 UK Biobank participants reveal 231,631 predicted loss-of-function variants (>10-fold more than imputed data); burden tests implicate PIEZO1, MEPE, and COL6A1 in disease traits.

GLnexus, a joint variant caller backed by an incrementally growable gVCF database, largely matched GATK on 50,000 exomes while keeping more rare indels and using 3.8–6.6-fold fewer core-hours.

The paper analyzes cryptic relatedness in a large exome cohort, identifies numerous close relationships, reconstructs pedigrees, and demonstrates their utility in improving mutation phasing and identifying de novo mutations.

KaryoScan detects chromosomal anomalies from whole-exome sequencing, identifying aneuploidies and complex rearrangements in large cohorts.

The paper identifies and analyzes exonic copy number variants (CNVs) in 50,726 DiscovEHR participants, linking them to clinical traits and phenotypes.