fine-mapping

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.

Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep

The paper evaluates regional heritability mapping methods to identify QTLs in Soay sheep, finding that some methods detect new trait-associated regions not found by GWAS.

Genetic Gains from Sixty Years of Spring Wheat Breeding in the Northern Plains of the US

This study quantifies genetic gains in HRS wheat over 60 years, finding annual yield gains of 0.61% but no improvement in grain protein since 1995.

Robust inference and widespread genetic correlates from a large-scale genetic association study of human personality

This study identifies 1,257 genetic variants associated with human personality traits using large-scale GWAS and finds widespread genetic correlations with behaviors and life outcomes.

Accounting for uncertainty in residual variances improves calibration of the Sum of Single Effects model for small sample sizes

The paper modifies the SuSiE model to improve calibration in small-sample studies, reducing false positives in genetic fine-mapping.

Genetic architecture and cellular basis of flag leaf size variation in barley

This study identifies genetic loci and cellular mechanisms underlying flag leaf size variation in barley using a multi-parent population and fine mapping.

The genetic architecture of cell-type-specific cis-regulation in maize

The paper identifies cell-type-specific cis-regulatory variants in maize using single-cell genomics and population genetics, revealing their role in local adaptation and flowering.

Improved genetic discovery and fine-mapping resolution through multivariate latent factor analysis of high-dimensional traits

The paper introduces a method to improve genetic discovery and fine-mapping by analyzing latent factors from high-dimensional traits, showing enhanced power compared to traditional approaches.

Peruvian Population Genomics: Unraveling the Genetic Landscape and Admixture Dynamics of Urban Populations

The paper analyzes genome-wide data from 432 Peruvian urban individuals to reveal fine-scale population structure, admixture dynamics, and demographic patterns shaped by ancient and recent events.

Integration of functional genomics and statistical fine-mapping systematically characterizes adult-onset and childhood-onset asthma genetic associations.

This study integrates functional genomics and statistical fine-mapping to identify causal variants, regulatory elements, and effector genes for adult-onset and childhood-onset asthma.

Genetic basis of an adaptive polymorphism controlling butterfly silver iridescence

This study identifies the genetic basis of silver iridescence polymorphism in Mormon Fritillary butterflies, linking it to the optix gene and showing evidence of selection and introgression.

Identification of genetic variation associated with high-temperature tolerance in cowpea

This study identifies genetic variants linked to heat tolerance in cowpea using envGWAS and allele frequency outlier analysis across 580 accessions, highlighting the association between high temperature and low precipitation traits.

Genome-wide association study in European beech (Fagus sylvatica L.) for drought stress traits

The paper conducts a GWAS in European beech to identify genetic markers associated with drought stress traits, finding significant SNPs linked to stomatal density and water use efficiency.

Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction

This study improves antigen specificity prediction by fine-tuning pre-trained antibody language models on SARS-CoV-2 and influenza antigens, showing better accuracy than models trained on embeddings alone.

Optimizing UK Biobank Cloud Based Research Analysis Platform to Fine Map Coronary Artery Disease Loci in Whole Genome Sequencing Data

The paper fine maps CAD loci in UK Biobank whole genome sequencing data using PolyFun and ML tools, showing improved sensitivity over traditional methods and demonstrating cost and speed benefits of cloud-based analysis.

Brain and Blood Transcriptome-Wide Association Studies Identify Five Novel Genes Associated with Alzheimer's Disease

Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses

The paper introduces efficient algorithms for fine-scale local ancestry inference using haplotypes, revealing recent selection on immune-related genomic regions in the UK Biobank.

Leveraging nationwide health care records in Estonia to identify the genetic background of understudied disease phenotypes

The paper uses Estonian Biobank data to identify genetic loci associated with 5,491 disease phenotypes, finding 3,222 genome-wide significant loci and 754 protein-altering variant-trait associations.

Genotype-Epigenome-Phenotype Integration Reveals the Contributions of Peripheral Immune Cells to Bipolar Disorder Pathogenesis, Phenotypic Heterogeneity, and Therapy

This study integrates genotype, epigenome, and phenotype data to show immune cells contribute to bipolar disorder pathogenesis, heterogeneity, and therapy through epigenomic and genetic mechanisms.

Novel Parkinson's Disease Genetic Risk Factors Within and Across European Populations

A cross-European Parkinson's disease GWAS meta-analysis of 63,555 cases, 17,700 proxy cases and 1,746,386 controls finds 134 risk loci (59 novel), 157 independent signals, and brain-enriched risk genes.

Immune-developmental processes contribute to schizophrenia risk: insights from a genetic overlap study with height

This study identifies 142 genes associated with both schizophrenia and height, finding enrichment in immune response genes and partial genetic overlap with white blood cell count.

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.

Integration of Deep Learning Annotations with Functional Genomics Improves Identification of Causal Alzheimers Disease Variants

This paper improves identification of causal Alzheimer's disease variants by integrating deep learning annotations with functional genomics, resulting in better fine-mapping and polygenic risk prediction across diverse populations.

Mechanistic Heterogeneity in Type 2 Diabetes and Hypertension Comorbidity Revealed with Partitioned Polygenic Scores

The paper identifies genetic clusters underlying T2D and hypertension comorbidity using partitioned polygenic scores, improving risk prediction for individuals with heightened susceptibility.

Cross-ancestry genome-wide association study and systems-level integrative analyses implicate new risk genes and therapeutic targets for depression

This study identifies 287 depression risk loci, 140 new, through cross-ancestry GWAS and integrates functional and pathway analyses to highlight potential therapeutic targets.

Identification of QTLs linked to partial resistance to foot and root rot caused by Fusarium avenaceum and Fusarium oxysporum in faba bean (Vicia faba)

The paper identifies a QTL linked to partial resistance to Fusarium foot and root rot in faba bean using a biparental mapping population.

IQI: Individualized Quantitative trait loci (QTL) Index

The paper introduces IQI, an individualized QTL index, to detect and characterize differences in QTL effects across individuals and populations, enabling more precise genetic analysis.

ESM-Effect: An Effective and Efficient Fine-Tuning Framework towards accurate prediction of Mutation's Functional Effect

ESM-Effect is a fine-tuning framework for predicting mutation functional effects, achieving state-of-the-art performance and faster training than multi-modal methods.

Fine-mapping reveals four TMEM106B haplotypes associated with neurodegenerative risk and preserved cognition at extreme age

Genetic regulation of the vascular endothelial growth factor receptor 1 during sepsis and association with ARDS susceptibility

This study identifies pQTLs of sVEGFR1 levels during sepsis and links them to ARDS susceptibility and mortality using GWAS, colocalisation, and Mendelian randomisation.