L. Adrienne Cupples

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.

This study investigates the association between mosaic loss of Y chromosome (mLOY) and lung function, emphysema, and epigenetic aging in men across multiple cohorts.

The paper identifies genes associated with obesity risk loci by integrating genetic and transcriptomic data from blood and brain tissues.

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

The paper introduces a framework for detecting noncoding rare variant associations using whole-genome sequencing data, applying it to lipid traits in the TOPMed program.

The paper performs whole genome sequence analysis of plasma lipid levels in 66,329 individuals, identifying new lipid-associated alleles, including rare non-coding variants.

The paper performs whole genome sequence association analysis of fasting glucose and insulin levels in diverse cohorts, identifying 22 significant variants across 16 gene regions, including rare variants.

The paper uses bidirectional Mendelian randomization to show LTL lengthening increases CHIP risk, while CHIP accelerates LTL shortening, with modest mediation between CHIP and CAD via LTL.

This study identifies 35 genes associated with circulating lipid levels using rare coding variants from 170,000 exomes across multiple ancestries.

The paper reports whole-genome association analyses of sleep-disordered breathing traits in the NHLBI TOPMed program, identifying rare and common variant associations.

The paper examines the concordance and characteristics of mitochondrial heteroplasmic mutations in maternal pairs of European and African ancestry, finding higher concordance in close relatives and associations with age and nuclear genome regions.

The paper uses whole genome sequencing to identify genetic loci associated with platelet aggregation, including novel variants in RGS18, SVEP1, and PEAR1.

The paper introduces BinomiRare, a test for rare variant association with binary outcomes in mixed models, showing it controls type 1 error in simulations and applies it to study genetic variants in disease traits.

The paper describes a system for harmonizing phenotype data across multiple studies in the TOPMed program, enabling reproducible and shared phenotype data for over 80 studies.

This paper introduces RUTH, a new HWE test that accounts for population structure and genotype uncertainty, showing it reduces false positives compared to traditional methods.

The paper evaluates methods to handle missing lifestyle data in gene-by-lifestyle interaction meta-analyses and recommends the Safe Approach for accuracy.

This study identifies 59 sentinel variants and two novel genes associated with telomere length using whole genome sequences from 109,122 trans-ethnic individuals.

The paper identifies rare non-coding variants from whole genome sequencing in the TOPMed program, showing they contribute significantly to type 2 diabetes heritability.

This study identifies DNA methylation sites associated with central adiposity traits in adults and adolescents using methylome-wide association analyses across multiple cohorts.

The paper addresses variance stratification in pooled whole genome sequencing data, showing how study-specific phenotypic variances affect analysis and introducing a method to improve statistical power and reduce false positives.

The paper analyzes gene-environment interaction effects across multiple ancestries and traits, identifying population-specific genetic mechanisms and methodological biases in GxE studies.

This study uses TOPMed whole genome sequences to improve imputation quality and detect rare variant associations in admixed African and Hispanic/Latino populations, identifying two novel associations with hematological traits.

The paper identifies germline genetic variants associated with clonal hematopoiesis of indeterminate potential (CHIP) using whole genome sequences from the TOPMed program.

The paper identifies genetic variants affecting HbA1c levels in multi-ancestry cohorts, showing ancestry-specific impacts on diabetes diagnosis via HbA1c.

The paper identifies loss-of-function variants affecting liver-related blood traits that reduce CVD risk without increasing metabolic disease risk, highlighting potential therapeutic targets.

The paper introduces a fully-adjusted two-stage method for rank normalization in genetic association studies to reduce Type I errors and improve power by adjusting for covariates in both stages.

The paper introduces SMMAT, a variant-set mixed model association test for continuous and binary traits in large-scale WGS studies, showing it controls type I error rates and applies to population structured and related samples.

The paper analyzes whole genome sequences from 16,324 individuals to identify genetic variants associated with blood lipid levels and develops a polygenic score for LDL-C.

The paper uses whole genome sequencing to identify genetic variants associated with plasma lipoprotein(a) levels and finds high heritability and inter-ethnic differences in Lp(a) risk.

The paper describes the quality control and integration of genotype calls from two pipelines for whole genome sequencing data in the Alzheimer’s Disease Sequencing Project, resulting in a high-quality consensus dataset.