Anurag Verma

ARCHER-LD: Rapid Long-Range Linkage Disequilibrium Calculations at Biobank Scale using GPU Acceleration

The paper introduces ARCHER-LD, a GPU-accelerated method to compute long-range linkage disequilibrium at biobank scale, achieving significant speedups over existing tools.

A Computational and Statistical Framework Leveraging AI-Derived CT Phenotypes for Causal Mediation Effects Between Genetic Variants and Disease

This paper uses GWAS and mediation analysis on CT-derived phenotypes to show genetic variants influence disease through intermediate imaging traits.

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses

The PMBB Geno-Pheno Toolkit provides modular pipelines for cross-biobank association analyses, supporting GWAS, ExWAS, and PheWAS with containerized workflows.

Genetic drivers of etiologic heterogeneity in thyroid cancer

This study identifies 51 genetic loci associated with thyroid cancer through a multi-ancestry GWAS and explores pleiotropic relationships to uncover mechanistic clusters and genetic subtypes.

The Biobank Rare Variant consortium powers the discovery of rare genetic associations through global collaboration

The paper establishes a global consortium to discover rare genetic associations by integrating data from multiple biobanks, identifying 514 gene-trait associations, many detectable only through cross-ancestry meta-analysis.

Multi-ancestral GWAS with the VA Million Veteran Program enables functional interpretation of rheumatoid arthritis alleles

This study conducts a multi-ancestry GWAS of rheumatoid arthritis using the VA Million Veteran Program, identifying 152 genome-wide significant loci and improving fine-mapping resolution.

DRIVE-KG: Enhancing variant-phenotype association discovery in understudied complex diseases using heterogeneous knowledge graphs

DRIVE-KG integrates multi-omics data into a knowledge graph to discover SNP-phenotype associations and predict endometriosis status, uncovering new variant-phenotype links and improving classification performance.

Endophenotype-Informed Polygenic Risk Stratification for Primary Open-Angle Glaucoma in individuals of African Ancestry

This paper develops endophenotype-informed polygenic risk scores for POAG in African ancestry individuals, showing improved clinical interpretability and risk stratification compared to aggregate scores.

Leveraging Open-Source Large Language Models to Identify Undiagnosed Patients with Rare Genetic Aortopathies

This paper develops an open-source LLM-based pipeline to identify patients with rare genetic aortopathies using clinical notes, achieving high accuracy in recommending genetic testing.

Large-scale evaluation of proteomic and polygenic risk scores reveals complementary contributions to incident disease prediction

The paper evaluates proteomic and polygenic risk scores for disease prediction, finding proteomic scores outperform polygenic scores in most traits and show temporal responsiveness.

Genome-wide Association Study of Long COVID

This study performs a genome-wide association study for Long COVID, identifying a significant association with the FOXP4 locus and highlighting the role of pulmonary dysfunction and COVID-19 severity.

Genome-Wide Assessment of Pleiotropy Across >1000 Traits from Global Biobanks

The paper identifies pleiotropic loci across 1,167 traits using GWAS meta-analysis and shows they are enriched for functional annotations and improve polygenic score predictions.

Population Performance and Individual Agreement of Coronary Artery Disease Polygenic Risk Scores

This study evaluates the reliability of coronary artery disease polygenic risk scores across diverse populations, finding poor individual agreement despite equivalent population-level performance.

Diversity and Scale: Genetic Architecture of 2,068 Traits in the VA Million Veteran Program

Population-stratified GWAS of 2,068 traits in 635,969 Million Veteran Program participants, 29% genetically non-European, yields 98,485 associations and 57,601 fine-mapped signals with largely shared cross-population architecture.

Accelerating Genome- and Phenome-Wide Association Studies using GPUs - A case study using data from the Million Veteran Program

This paper optimizes the SAIGE algorithm using GPUs to accelerate GWAS on large datasets, achieving 20x speedup on the Million Veteran Program data.

Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network

This study constructs an augmented disease network incorporating genetic correlations with endophenotypes to uncover genetic associations across diseases and biomarkers.

Genome-wide association meta-analysis identifies novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation

This study identifies ancestry-specific and sex-specific genetic loci for primary open-angle glaucoma through a meta-analysis of 15 biobanks, highlighting shared biology with vascular mechanisms and cell proliferation.

The genetic and phenotypic correlates of mtDNA copy number in a multi-ancestry cohort

This study investigates mtDNA copy number (mtCN) in a diverse cohort, finding ancestry-specific genetic and phenotypic associations and highlighting the impact of blood cell composition on results.

Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population

The paper evaluates the frequency and impact of pharmacogenetic alleles in a diverse biobank population, finding high prevalence of actionable alleles and disparities by ancestry.

Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

This paper shows that meta-analysis fine-mapping is often miscalibrated due to cohort heterogeneity and introduces a QC method to identify suspicious loci.

Global Biobank Meta-analysis Initiative: powering genetic discovery across human diseases

Meta-analysis of harmonized GWAS from up to 18 biobanks (six ancestry groups) across 14 endpoints replicated 320 known loci and identified 188 apparently novel loci.

Genetic regulation of OAS1 nonsense-mediated decay underlies association with risk of severe COVID-19

The paper identifies a Neandertal introgressed haplotype in the OAS1 gene associated with increased risk of severe COVID-19 and shows it impairs SARS-CoV-2 clearance through genetic regulation of OAS1 expression.

A trans-ancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation.

This study conducts a trans-ancestry GWAS using chronic ALT elevation as a proxy for NAFLD, identifies 77 significant loci, and validates 17 SNPs with histology and imaging data, revealing genetic links to metabolic and inflammatory traits.

Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection.

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.

A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program

This study identifies genetic variants associated with severe COVID-19 and finds shared genetic architecture with complex diseases using EHR data from the Million Veteran Program.

Genome-wide analysis in 756,646 individuals provides first genetic evidence that ACE2 expression influences COVID-19 risk and yields genetic risk scores predictive of severe disease

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

hudson: A User-Friendly R Package to Extend Manhattan Plots

hudson extends Manhattan plots for genome-wide studies with interactive features and flexible frameworks for various analyses.

Alternative splicing of OAS1 alters the risk for severe COVID-19

The paper identifies an alternative splicing variant of OAS1 that provides protection against severe COVID-19 in people of African ancestry, independent of Neanderthal haplotypes.

Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank

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.

Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data

The paper uses multi-ancestry biobank data and integrative methods to identify gene-disease associations across different ancestry groups, finding shared and ancestry-specific genetic links.