Peter Kraft

Genetic and Cellular Architecture of Breast Cancer Risk Across Ancestries

This study analyzes breast cancer GWAS across multiple ancestries, finding similar heritability and genetic correlations, and identifies shared regulatory and cellular contexts.

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.

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.

Phenome-derived polygenic scores and social determinants jointly shape context-dependent disease risk

This paper constructs phenome-derived polygenic scores and evaluates how they, along with social determinants of health, influence disease risk across different populations and diseases.

Evaluating Multi-Ancestry Genome-Wide Association Methods: Statistical Power, Population Structure, and Practical Implications

This study compares pooled analysis and meta-analysis for multi-ancestry GWAS, finding pooled analysis offers better statistical power while controlling population structure.

Genome-wide association studies in a large Korean cohort identify novel quantitative trait loci for 36 traits and illuminate their genetic architectures

This study conducts GWAS in a large Korean cohort, identifying 301 novel loci and highlighting East Asian-specific genetic associations for 36 traits.

Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification

The paper uses case-control data from over 400,000 women to classify BRCA1 and BRCA2 variants, finding high consistency with ClinVar annotations for 785 previously unclassified variants.

Association of Gene Variant Type and Location with Breast Cancer Risk in the General Population

This study evaluates breast cancer risks associated with pathogenic variant type and location in BRCA2 and other genes, finding differential risks based on variant position.

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.

Genomic and proteomic evidence for hormonal and metabolic foundations of polycystic ovary syndrome

This study identifies 31 plasma proteins and expands genetic loci associated with PCOS, highlighting metabolic and hormonal influences and polygenic risk effects on cardio-metabolic outcomes.

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

This study identifies 43 genomic loci associated with reproductive success in 785,604 individuals, showing ongoing natural selection at the FADS locus.

A genome-wide association study of mammographic texture variation

This paper identifies genetic loci associated with mammographic texture variation and finds significant genetic correlations with breast cancer risk and mammographic density.

Polygenic Risk Scores for Prediction of Breast Cancer in Korean women

This paper evaluates polygenic risk scores for breast cancer prediction in Korean women, finding that combining Asian and European PRS improves discrimination over lifestyle factors.

Cross-Ancestry Investigation of Venous Thromboembolism Genomic Predictors

This study identifies 135 genomic loci associated with venous thromboembolism risk through cross-ancestry GWAS and provides insights into biological pathways and potential therapeutic targets.

Germline cancer gene expression quantitative trait loci influence local and global tumor mutations

The paper identifies germline variants that influence somatic mutations in cancer genes through expression regulation across multiple cancer types.

A framework evaluating the utility of multi-gene, multi-disease population-based panel testing that accounts for uncertainty in penetrance estimates

The paper presents a framework to evaluate the clinical utility of multi-gene, multi-disease panel testing by incorporating variant frequency, penetrance estimates, and disutilities, while accounting for uncertainty in penetrance.

Somatic mutational profiles and germline polygenic risk scores in human cancer

This study examines associations between somatic mutational profiles and germline polygenic risk scores in 12 cancer types, finding 17 significant links after correction.

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

Pancreatic cancer risk predicted from disease trajectories using deep learning

This paper uses deep learning to predict pancreatic cancer risk from clinical disease trajectories in two large datasets, achieving higher accuracy than models without temporal information.

Rare copy number variants (CNVs) and breast cancer risk

The paper analyzes rare copy number variants (CNVs) in breast cancer cases and controls, identifying associations with known and novel susceptibility loci.

Leveraging expression from multiple tissues using sparse canonical correlation analysis (sCCA) and aggregate tests improves the power of transcriptome-wide association studies (TWAS)

This paper improves transcriptome-wide association study (TWAS) power by integrating multiple tissues using sparse canonical correlation analysis (sCCA) and aggregate tests, identifying more gene-trait associations.

Estimating the effective sample size in association studies of quantitative traits

This paper introduces an analytical method to estimate effective sample size in mixed-model GWAS of quantitative traits, showing its performance in unrelated and related individuals.

Improving reporting standards for polygenic scores in risk prediction studies

ClinGen and the PGS Catalog expand the GRIPS guideline into a 22-item Polygenic Risk Score Reporting Statement covering study populations, model construction, evaluation, and clinical interpretation.

Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers

This study assesses polygenicity and risk prediction using common variants across 14 cancers, finding varying numbers of susceptibility variants and risk score effectiveness.

Multitrait genetic-phenotype associations to connect disease variants and biological mechanisms

The paper decomposes multitrait genetic associations to identify pleiotropy profiles linking SNPs to biological pathways and drug targets.

A large cross-ancestry meta-analysis of genome-wide association studies identifies 69 novel risk loci for primary open-angle glaucoma and includes a genetic link with Alzheimer's disease

A polygenic and phenotypic risk prediction for Polycystic Ovary Syndrome evaluated by Phenome-wide association studies

This study develops a polygenic and phenotypic risk score for PCOS using EHR data, showing improved detection and identifying shared metabolic and endocrine comorbidities.

Mixed-model admixture mapping identifies smoking-dependent loci of lung function in African Americans

The paper uses admixture mapping to identify smoking-dependent loci affecting lung function in African Americans, finding two genome-wide significant loci associated with ancestry-smoking interactions.

Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic

This paper introduces the Generalized Berk-Jones statistic for gene set analysis in GWAS, showing it increases power by incorporating multiple signals per gene and addressing confounding from gene set lists.

Genome-wide association study of anti-Mullerian hormone levels in pre-menopausal women of late reproductive age and relationship with genetic determinants of reproductive lifespan

This study identifies a genetic variant associated with AMH levels in pre-menopausal women and links AMH to reproductive lifespan.