polygenic risk

FastHer: a fast and accurate estimator of local heritability from GWAS summary statistics

FastHer provides a fast and accurate method for estimating local heritability from GWAS summary statistics, achieving GREML-level accuracy with significantly reduced computational time.

Deciphering the Genomic architecture of three major Cancers in African-Ancestry Populations

This study identifies cancer risk loci and genetic architectures in African-ancestry populations using GWAS and PRS, highlighting disparities in predictive performance across cancers.

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats

The paper identifies host genetic effects on microbiome composition in rats and finds evidence of indirect genetic effects contributing to missing heritability.

Ancient genomes from the siege and destruction of Middle Bronze Age Roca Vecchia (Apulia, Italy) shed light on Aegean contacts and conflicts

The paper analyzes ancient genomes from Roca Vecchia to determine genetic contributions from Minoans and local populations during the Bronze Age.

High-Coverage Jomon Genomes Provide Insights into Population Structure and Genetic Traits of Ancient Japanese Hunter-Gatherers

This study analyzes eight high-coverage Jomon genomes to reveal genetic continuity and phenotypic traits of ancient Japanese hunter-gatherers, showing their genetic influence on present-day Japanese populations.

Modifiable lifestyle factors and genetic risk of obesity in Indians

This study shows that individuals of Indian ancestry with high genetic risk for obesity can reduce their risk through favorable lifestyle choices, as demonstrated in two cohorts.

GENPHIRE: Enhancing Disease Risk Prediction Using Large Language Model

GENPHIRE uses a large language model to convert genotype profiles into embedded vectors for disease risk prediction, outperforming existing polygenic risk scores in UK Biobank data.

Quantifying the susceptibility of polygenic scores to ancestry stratification

This paper quantifies how polygenic scores are affected by ancestry stratification using a theoretical framework and applies it to UK Biobank data.

Improving polygenic risk prediction performance through integrating electronic health records by phenotype embedding

This paper introduces EEPRS, a framework that improves polygenic risk prediction by integrating electronic health records through phenotype embeddings, showing significant performance gains over traditional methods.

S4-Multi: enhancing polygenic score prediction in ancestrally diverse populations

S4-Multi improves polygenic score prediction across diverse ancestries by reducing genetic variants while maintaining accuracy in non-European populations.

Modeling nonlinear and interaction effects of spatiotemporal and other non-genetic factors improves phenotypic prediction for complex traits

Adaptive Partial Conjunction Hypothesis: Identifying Pleiotropy Across Heterogeneous Effect Units

The paper introduces APCH, a method to identify pleiotropy across multiple traits and tissues by modeling heterogeneous effect sizes and subset-level inference.

Improving type 2 diabetes polygenic risk scores by incorporating rare, low-frequency, and population-specific variants

This paper improves type 2 diabetes polygenic risk scores by including rare and population-specific variants, showing better risk prediction in diverse populations.

Imputation Disparities Driven by Recent Selectionand Their Impact on Disease Risk Estimation in East and Southeast Asian Populations

The paper evaluates imputation performance in East and Southeast Asian populations, showing that recent selection affects variant detection and polygenic risk score estimation.

Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry

The paper identifies non-coding SNPs associated with prostate cancer risk in men of African ancestry using a deep learning model and experimental validation.

PRISM: ancestry-aware integration of tissue-specific genomic annotations enhances the transferability of polygenic scores

PRISM improves polygenic score transferability across populations by integrating ancestry-aware tissue-specific genomic annotations, achieving a 13.10% performance boost for African ancestry.

ImputePGTA: accurate embryo genotyping and polygenic scoring from ultra-low-pass sequencing

ImputePGTA improves embryo genotyping and polygenic scoring from ultra-low-pass sequencing by jointly inferring inheritance and parental haplotype phasing.

Kinship estimation bias carries over to heritability estimation bias using variance components

This study shows that biased kinship estimation in structured populations leads to heritability estimation bias, with Popkin being the only unbiased estimator.

The Role of Genomic-Informed Risk Assessments in Predicting Dementia Outcomes

This paper constructs a genomic-informed dementia risk score combining genetic and clinical factors and finds that most memory clinic patients have at least one high-risk indicator, with higher burden linked to increased dementia risk.

Real-time dynamic polygenic prediction for streaming data

This paper introduces rtPRS-CS, a real-time polygenic risk score method that dynamically updates predictions as new data streams in, improving accuracy for schizophrenia risk across diverse populations.

Within- and Between-Family Validation of Nine Polygenic Risk Scores Developed in 1.5 Million Individuals: Implications for IVF, Embryo Selection, and Reduction in Lifetime Disease Risk

The paper validates nine polygenic risk scores in family and multi-ancestry datasets, showing their potential to reduce disease risk through embryo selection in IVF.

MAP-PRS: Multi-Ancestry Portfolio-Based Polygenic Risk Scores

MAP-PRS improves polygenic risk score fairness and reliability across populations by combining ancestry-specific models with portfolio optimization and computational tools.

Sparse Polygenic Risk Score Inference with the Spike-and-Slab LASSO

This paper introduces SSLPRS, a Polygenic Risk Score method using Spike-and-Slab LASSO, showing improved variable selection and prediction accuracy over existing methods.

Population-Specific Polygenic Risk Scores Developed for the Han Chinese

The paper develops population-specific polygenic risk scores for Han Chinese using genomic and electronic health record data, showing strong predictive performance for multiple diseases.

The Taiwan Precision Medicine Initiative: A Cohort for Large-Scale Studies

The Taiwan Precision Medicine Initiative (TPMI) recruits a large cohort for genetic and electronic medical record studies to advance precision medicine.

Polygenic prediction of treatment efficacy with causal transfer learning

This paper introduces a statistical framework to identify genetically driven heterogeneous treatment effects using causal transfer learning, applied to RCTs to find key determinants of treatment efficacy.

Adaptive prediction intervals for polygenic risk scores reveal individual variation in genetic predictability

This paper introduces a framework for quantifying uncertainty in polygenic risk scores, showing that prediction intervals vary with genetic and environmental factors.

Benchmarking non-additive genetic effects on polygenic prediction and machine learning-based approaches

This study benchmarks the impact of non-additive genetic effects on polygenic prediction and machine learning approaches using simulated and real data.

Hidden structure in polygenic scores and the challenge of disentangling ancestry interactions in admixed populations

This paper examines how genetic interactions with ancestry affect polygenic scores and shows that models of local and global ancestry interactions can be distinguished using partial polygenic scores when causal variants are known.

Prediction of Polygenic Risks by Screening Thousands of Polygenic Scores

The paper introduces SECRET, a method to develop polygenic scores for traits with limited data, showing improved prediction power over existing methods.