GWAS summary statistics

Evaluating the Impact of Principal Component and Mixed Model Approaches on Polygenic Risk Score Portability to Diverse Ancestries in the UK Biobank

This study evaluates how principal component and mixed model approaches affect polygenic risk score portability across different ancestries in the UK Biobank.

Estimating uncertainty in family-based GWAS

This study investigates uncertainty in sibling-based GWAS allelic effect estimates and proposes a resampling-based method that is more accurate than existing approaches.

Genomic analysis identifies polygenic and region-specific contributions to ADHD-migraine comorbidity

This study identifies shared genetic variants and gene expression mechanisms between ADHD and migraine using genome-wide association data and multiple genetic analyses.

Genome-wide analyses reveal shared and distinct genetic architecture linking amyotrophic lateral sclerosis, sporadic frontotemporal dementia and cognitive traits

The paper identifies shared and distinct genetic loci linking ALS, sFTD, and cognitive traits using genome-wide association data.

When the Background Matters: Topic-Dependent reference lists in GWAS and Exome Analyses

The paper shows that using mismatched genome or exome backgrounds in GO analysis affects significance and introduces annotation bias, with practical implications for GWAS and WES studies.

PubMind: Literature-Based Genetic Variant Extraction and Functional Annotation Using Large Language Models

PubMind extracts and annotates genetic variant functionality from biomedical literature using LLMs, creating a database with over 1.3 million variants.

Representation in genetic studies affects inference about genetic architecture

Across UK Biobank, All of Us and FinnGen, the inferred mean direction (sign bias) of rare minor-allele effects varies and is largely explained by each cohort's trait skewness.

Benchmarking Bayesian colocalization methods in validating Mendelian randomization-identified targets

This study benchmarks four Bayesian colocalization methods to validate MR-identified protein-trait associations for cardiometabolic traits, finding SharePro most frequently supports significant associations.

Genome-wide association study of corneal dystrophy uncovers novel risk loci and enables improved polygenic prediction of Fuchs endothelial corneal dystrophy

This paper identifies 24 risk loci for corneal dystrophy, constructs polygenic risk scores (PRS) and STR-based models, and shows PRS improves FECD prediction, while STR expansion is the strongest predictor.

Cannabis use and Cancer: Dissecting genetic causality for site-specific risks through two-sample Mendelian Randomization

This study uses Mendelian randomization to assess causal links between cannabis use and site-specific cancers in Europeans, finding associations with esophageal, lung, and protective effects against pancreatic cancer.

Estimating genetic correlation jointly using individual-level and summary-level GWAS data

This paper introduces GENJI, a method to estimate genetic correlation using both individual-level and summary-level GWAS data, improving accuracy and efficiency over existing methods.

Inferring causal cell types of human diseases and risk variants from candidate regulatory elements

This paper introduces CT-FM and CT-FM-SNP methods to identify causal cell types and variants for diseases, finding most SNPs affect traits via a single cell type set.

plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics

plinkQC is an R package that performs ancestry inference, sample selection, and quality control in population genetics, achieving 98% accuracy with minimal marker overlap.

Mendelianization: Concentrating Polygenic Signal into a Single Causal Locus

Mendelianization concentrates polygenic signals into a single causal locus to improve interpretability of complex disorders.

Copy number variant association analysis in 94,730 Chinese adults reveals loci influencing anthropometric and cardiometabolic traits

This study identifies 19 CNV associations with anthropometric and cardiometabolic traits in 94,730 Chinese adults, expanding ancestry diversity in CNV research.

TRIDENT: a framework for robust multi-trait GWAS identifies 66 novel multi-trait osteoarthritis signals

TRIDENT is a framework for robust multi-trait GWAS that identifies 66 novel osteoarthritis signals by combining earlier and larger GWAS meta-analyses and applying translational annotation.

Integrating Genomic and Proteomic Data Improves Complex Trait Prediction in Diverse Populations

This study integrates polygenic risk scores and proteomic risk scores to improve prediction of complex traits across diverse populations.

SuSiNE: Genetic fine-mapping with signed functional priors and multi-basin ensembling

SuSiNE improves genetic fine-mapping by incorporating signed functional priors and multi-basin ensembling to better resolve LD ambiguity and uncertainty.

A Novel Method to Disentangle Tightly Linked Risk and Resilience Genes for Brain Disorders Application to Alzheimers Disease

The paper introduces an adversarial neural network to identify genetic resilience markers in Alzheimer's disease, finding five SNPs associated with resilience independent of polygenic risk scores.

Genotype-predicted drug response phenotypes and their co-occurrence with dispensed medicines among 738,531 participants in the UK Our Future Health study

The paper assesses the co-occurrence of actionable pharmacogenomic phenotypes with dispensed medicines in 738,531 UK participants, finding 36.8% had gene-matched medications.

Large-scale admixture mapping in the All of Us Research Program improves the characterization of cross-population phenotypic differences

The paper uses admixture mapping in the All of Us Research Program to identify genetic ancestry associations with 22 traits, finding 71 novel loci where African ancestry explains phenotypic variation.

A unified framework for local-ancestry-aware genetic association analysis across biobanks

FELIX improves genetic association analysis by accounting for local ancestry in admixed populations, increasing significant loci and improving polygenic score prediction.

Uveal and cutaneous melanoma share a common mutation with distinct prognostic implications: A bioinformatic study

This study identifies two shared genetic variants between uveal and cutaneous melanoma and suggests IRF4 as a common prognostic biomarker.

PANACEA: a framework to maximise genetic diversity in genome-wide association study meta-analyses

PANACEA improves GWAS meta-analysis by using a continuous ancestry representation to include more diverse participants and increase statistical power.

Uncovering High-Order Epistatic Interactions in GWAS via a Machine Learning-Based Feature Engineering Framework

The paper introduces a machine learning framework to detect high-order genetic interactions in GWAS by encoding decision paths from classification trees as features, improving model accuracy and interpretability.

Assessing Computational Models for Pharmacogenomic Variant Interpretation

This study evaluates computational models for predicting pharmacogenomic variant effects, finding that StructureDCA outperforms other methods in distinguishing functional variants.

Using summary data to detect and quantify ascertainment in biobanks

This paper introduces a summary-statistics-based method to detect and quantify ascertainment bias in genetic studies using polygenic scores across multiple biobanks.

Multi-environment GWAS analysis for photosynthetic light use efficiency in Arabidopsis thaliana

This study performs multi-environment GWAS on photosynthetic light use efficiency in Arabidopsis thaliana, identifying robust and conditional quantitative trait loci.

Identification of Comprehensive Genetic Factors, Pathways, and Shared Genetic Architecture of Putamen Volume in Adolescent Cohort

The paper identifies genetic factors and pathways associated with putamen volume using GWAS data from the ABCD study and finds shared genetic architecture with neuropsychiatric disorders.

Lack of genetic evidence for a role of SLC25A46 in alpha-synucleinopathies

The paper investigates the genetic role of SLC25A46 in Parkinson's disease, REM sleep behavior disorder, and Dementia with Lewy Bodies, finding no significant associations.