Charles L Kooperberg

Clonal Hematopoiesis Accelerates Frailty and Functional Decline

This study links clonal hematopoiesis to accelerated frailty and functional decline across multiple organ systems in humans.

TorchGWAS2: Cost-Effective Phenome- and Genome-Wide Association Testing in Related Samples

TorchGWAS2 improves genome-wide association testing in related samples by using a deterministic variance-correction algorithm, achieving faster and more powerful results across large-scale omics data.

Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed

The paper analyzes expression and splicing quantitative trait loci (e/sQTL) across multiple tissues in the TOPMed dataset and finds that secondary e/sQTL signals are still discoverable, with many GWAS signals colocalizing with these e/sQTL.

An Efficient Lasso Framework for Admixture-Aware Polygenic Scores

HAUDI improves polygenic score construction for admixed populations by efficiently extending the GAUDI method to multi-way admixture with faster computation and better performance.

The expected polygenic risk score (ePRS) framework: an equitable metric for quantifying polygenetic risk via modeling of ancestral makeup

The paper introduces the expected polygenic risk score (ePRS) framework to address population stratification in polygenic risk score analysis by modeling ancestral makeup, showing it provides equitable risk quantification across diverse populations.

Novel Genetic Risk Loci for Pancreatic Ductal Adenocarcinoma Identified in a Genome-wide Study of African Ancestry Individuals

This study identifies novel genetic risk loci for pancreatic ductal adenocarcinoma in African ancestry individuals through admixture mapping and GWAS.

Local ancestry modulates gene expression: shifting our understanding of genetic regulation and disease association within and across populations

The paper identifies ancestry-specific eQTL effects in Hispanic/Latino and African American populations, showing how local ancestry influences gene expression and disease risk.

Trans-Ancestry GWAS of Hot Flashes Reveals Potent Treatment Target and Overlap with Psychiatric Disorders

This paper conducts a trans-ancestry GWAS of hot flashes, identifies TACR3 as a key genetic target, and finds genetic overlaps with psychiatric disorders.

cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions

cellSTAAR integrates single-cell ATAC-seq with whole-genome sequencing to enhance power and interpretation of rare variant association tests in non-coding regions.

Human Plasma Proteomic Profile of Clonal Hematopoiesis

The paper identifies plasma proteins associated with clonal hematopoiesis and links them to cardiovascular disease through proteomic and genetic analyses.

Clonal Hematopoiesis and Risk of Stroke: Evidence from Over 800,000 Individuals Across Three Cohorts

This study finds that clonal hematopoiesis (CHIP) increases stroke risk across multiple cohorts, with specific gene mutations and inflammatory markers like IL-1RAP modifying this risk.

Genetic Architecture and Analysis Practices of Circulating Metabolites in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program

The paper analyzes circulating metabolites using genome-wide association data from the TOPMed program, identifying 1,778 loci and highlighting sex-specific genetic contributions.

Genome-wide association study provides novel insight into the genetic architecture of severe obesity.

This study identifies novel genetic signals associated with severe obesity through GWAS and shows strong genetic overlap with BMI, highlighting shared comorbidities and lifestyle interactions.

Type 2 diabetes polygenic risk score demonstrates context-dependent effects and associations with type 2 diabetes-related risk factors and complications across diverse populations

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

The paper introduces MultiSTAAR, a statistical framework for multi-trait rare variant analysis in WGS studies, identifying new lipid trait associations in diverse populations.

Epigenome-wide association study meta-analysis of BMI in African American Adults

This study conducts an epigenome-wide association study (EWAS) meta-analysis of BMI in African American adults, identifying 208 significant CpGs and 54 DMRs associated with BMI, including novel and replicated findings.

Whole genome analysis of plasma fibrinogen reveals population-differentiated genetic regulators with putative liver roles.

This study uses whole genome sequencing to identify 18 novel genetic loci associated with plasma fibrinogen levels, including variants more common in African populations and linked to liver-related traits and disease.

Genetic mechanisms of 184 neuro-related proteins in human plasma

The paper identifies genetic regulators of 184 neuro-related proteins in human plasma and links them to disease traits and drug targets.

The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations

The paper develops a method to quantify somatic mutation burden in whole-genome sequencing data without paired-tissue samples and identifies genetic and phenotypic correlates of clonal hematopoiesis without known driver mutations.

Multi-ancestry polygenic risk scores for venous thromboembolism

This study develops multi-ancestry polygenic risk scores for venous thromboembolism using diverse GWAS data and shows improved predictive performance across European- and African-ancestry populations.

Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People with Type 2 Diabetes Mellitus

This paper conducts a multi-ancestry time-to-event GWAS to identify genetic variants associated with incident cardiovascular disease in people with type 2 diabetes, finding three novel loci and confirming known CAD variants.

MUSSEL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups

MUSSEL improves polygenic risk prediction across populations by integrating GWAS summary statistics and using Bayesian hierarchical modeling with ensemble learning.

Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations

Admix-kit provides tools for genetic analysis of admixed populations, enabling simulation, association testing, and polygenic scoring.

Genome-Wide Interaction Analysis with DASH Diet Score Identified Novel Loci for Systolic Blood Pressure

The paper identifies novel genetic loci associated with systolic blood pressure that interact with the DASH diet score through genome-wide interaction analysis.

Genetic association analysis of age of ischemic stroke onset: a caveat

The paper performs a GWAS in a case-only design to identify genetic loci influencing age at onset of ischemic stroke and finds a robust association with the APOE locus, suggesting potential survival bias rather than direct causation.

Whole genome association testing in 333,100 individuals across three biobanks identifies rare non-coding single variant and genomic aggregate associations with height

Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics

This paper introduces HAMSTA, a method to estimate heritability from admixture mapping summary statistics while adjusting for ancestral stratification bias, and applies it to African American datasets.

Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study

The paper identifies 83 rare lncRNA variant sets associated with blood lipid levels using WGS data from the TOPMed program and validates some in UK Biobank data.

Whole Genome Sequencing Based Analysis of Inflammation Biomarkers in the Trans-Omics for Precision Medicine (TOPMed) Consortium

The paper analyzes inflammation biomarkers using whole-genome sequencing from the TOPMed consortium, identifying both single-variant and rare variant associations with inflammatory traits.

Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes

The paper validates novel telomere length regulation genes POP5 and KBTBD6 identified through trans-ancestry GWAS using functional experiments in blood cells.