Jennifer A. Smith

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.

A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India

The paper constructs a large-scale LD and genotype imputation reference panel using whole-genome sequencing data from 2,680 Indian participants, improving imputation accuracy and polygenic risk score performance.

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.

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.

Whole genome sequence association analysis of brain structural volume measures in the NHLBI TOPMed Program highlights novel loci in diverse participants

This study uses whole-genome sequence data from diverse participants to identify novel genetic loci associated with brain structural volumes, highlighting the importance of diverse cohorts in uncovering genetic architecture.

Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians from India

The paper identifies AD-associated genes in South Asians using whole-genome sequence data and variant analysis, finding associations for APOE, PICALM, and TSPOAP1 with cognitive function.

Multi-ancestry transcriptome-wide association studies of cognitive function, white matter hyperintensity, and Alzheimer's disease

This paper conducts multi-ancestry transcriptome-wide association studies to identify genes associated with cognitive function, white matter hyperintensity, and Alzheimer's disease using gene expression data from European and African ancestry individuals.

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.

Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood

The paper identifies genetic and phenotypic correlates of mosaic loss of chromosome Y in blood using whole genome sequencing data from the TOPMed program.

Differential prediction performance between Caribbean- and Mainland-subgroups using state-of-the-art polygenic risk scores for coronary heart disease: Findings from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

This study evaluates polygenic risk scores for coronary heart disease in Hispanic/Latino subgroups, finding better performance in Mainland compared to Caribbean subgroups.

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.

A Large-Scale Genome-Wide Gene-Sleep Interaction Study in 732,564 Participants Identifies Lipid Loci Explaining Sleep-Associated Lipid Disturbances

This study identifies 17 genetic loci associated with sleep duration and lipid levels, offering potential druggable targets for dyslipidemia in individuals with sleep disturbances.

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.

Effect of APOE e4 and its modification by sociodemographic characteristics on cognitive measures in South Asians from LASI-DAD

The paper examines the effect of APOE ε4 and its interaction with sociodemographic factors on cognitive measures in South Asians from LASI-DAD, finding stronger associations in older adults and females.

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.

Structural variation across 138,134 samples in the TOPMed consortium

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

Exome Array Analysis of 9,721 ischemic stroke cases from the SiGN Consortium

The paper analyzes exome array data from 9,721 ischemic stroke cases to identify coding variants associated with stroke, finding 15 significant variants, including 13 novel associations.

Mosaic chromosomal alterations in blood across ancestries via whole-genome sequencing

This study uses whole-genome sequencing to analyze mosaic chromosomal alterations across diverse ancestries, finding higher rates in certain populations and associations with germline variants.

A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies

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 Construction of Multi-ethnic Polygenic Risk Score using Transfer Learning

This paper introduces TL-PRS, a transfer learning method for constructing polygenic risk scores across ancestries, achieving up to 42% average relative improvement in South Asian and African ancestry groups.

Whole genome sequence analysis of blood lipid levels in >66,000 individuals

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.

Genomic and phenomic landscape of clonal hematopoiesis in over a million ancestrally diverse participants

This study analyzes clonal hematopoiesis in over a million diverse individuals, identifying 72 genome-wide significant loci and linking CHIP to various phenotypes.

Whole Genome Sequence Association Analysis of Fasting Glucose and Fasting Insulin Levels in Diverse Cohorts from the NHLBI TOPMed Program

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.

A multi-ethnic polygenic risk score is associated with hypertension prevalence and progression throughout adulthood

This paper constructs a multi-ethnic polygenic risk score for hypertension and shows it is associated with hypertension prevalence, progression, and related clinical outcomes.

Bidirectional Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of intermediate potential

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.

Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits - the Hispanic/Latino Anthropometry Consortium

This study identifies novel genetic loci for BMI, height, and WHRadjBMI in Hispanic/Latino populations and shows the benefits of ancestral diversity in GWAS.

Recovery of trait heritability from whole genome sequence data

The paper estimates heritability for height and BMI using whole-genome sequence data and finds that rare variants contribute significantly to the missing heritability.

Genome-wide association study meta-analysis identifies three novel loci for circulating anti-Müllerian hormone levels in women

A system for phenotype harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program

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.

Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries

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.