fine-mapping

The application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study

The paper estimates the functional effects of KEGG pathways on bovine stature using SNP summary statistics from GWAS and mixed linear models.

Single-step genome-wide association study for susceptibility to Teratosphaeria nubilosa and precocity of vegetative phase change in Eucalyptus globulus

This study uses ssGWAS to identify SNP-trait associations linked to MLD resistance and phase change precocity in E. globulus, finding ssGWAS more effective than traditional GWAS methods.

Comparison of two multi-trait association testing methods and sequence-based fine mapping of six QTL in Swiss Large White pigs

The paper compares two multi-trait association methods and fine-maps six QTL in pigs, finding similar results between methods but highlighting potential missed QTL in multi-trait analyses.

Whole genome sequencing reveals fine-scale climate associated adaptive divergence near the range limits of a temperate reef fish.

The paper uses whole genome sequencing to identify climate-associated adaptive divergence in cunner fish across Atlantic Canada, revealing genomic regions linked to environmental variables.

Reconstructing the formation of Hmong-Mien genetic fine-structure

This study reconstructs the genetic fine-structure of Hmong-Mien speakers using genome-wide data, showing that genetic substructure aligns more with linguistic classification than geography.

Quantitative assessment of association between noncoding variants and transcription factor binding

The paper extends the TRACE method to incorporate variant data, identifying footprint-QTLs that correlate with transcription factor binding and regulatory variants.

Identification of a sex-specific genetic signature in dementia with Lewy bodies: a meta-analysis of genome-wide association studies

This paper performs a large meta-analysis of GWAS in dementia with Lewy bodies, identifying sex-specific genetic risk signals and highlighting the need for larger cohorts.

Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing

This study uses low-coverage sequencing and imputation to identify QTLs for wool traits in rabbits, finding six QTLs with phenotypic contributions up to 7.50%.

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases

The paper shows glucocorticoid exposure reveals the function of non-coding genetic variants linked to disease risk by influencing gene expression in relevant biological processes.

DrFARM: Identification and inference for pleiotropic gene in GWAS

DrFARM identifies pleiotropic gene variants by jointly analyzing genetic data and controlling false discovery rate, finding 288 new metabolite associations in a metabolic study.

Correcting for volunteer bias in GWAS uncovers novel genetic variants and increases heritability estimates

This paper develops WGWAS to correct volunteer bias in GWAS, uncovering novel genetic variants and increasing heritability estimates for specific phenotypes.

Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

This paper shows that meta-analysis fine-mapping is often miscalibrated due to cohort heterogeneity and introduces a QC method to identify suspicious loci.

High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk

The paper maps promoter interactions in human ILC3s using PCHi-C and links GWAS risk variants to target genes, identifying new autoimmune disease risk genes.

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.

A stop-gain variant in BTNL9 is associated with atherogenic lipid profiles

The paper identifies a stop-gain variant in BTNL9 associated with lower HDL-C and higher triglycerides in Polynesian populations.

Simple scaling laws control the genetic architectures of human complex traits

The paper develops a probabilistic model to explain genetic architectures of complex traits using scaling laws, finding that traits share similar selection coefficients but differ in scaling parameters.

Influences of rare copy number variation on human complex traits

This paper develops a computational method to detect rare CNVs in UK Biobank data, identifies 269 CNV-trait associations, and highlights novel gene-trait relationships.

A novel framework for analysis of the shared genetic background of correlated traits

SHAHER is a framework that identifies shared genetic factors across correlated traits using GWAS summary statistics, showing improved performance in simulations and real datasets.

Scalable Bayesian functional GWAS method accounting for multivariate quantitative functional annotations with applications to studying Alzheimer's disease

This paper introduces BFGWAS_QUANT, a scalable Bayesian functional GWAS method that improves variant prioritization in Alzheimer's disease by integrating multivariate quantitative annotations.

Generalization of Cortical MOSTest Genome-Wide Associations Within and Across Samples

The paper evaluates the replication of genome-wide association loci discovered using MOSTest across different cohorts and finds higher replication yields and rates compared to min-P.

Dispensing with unnecessary assumptions in population genetics analysis

TarGene is a statistical workflow that estimates effect sizes and epistatic interactions without parametric assumptions, validated on UK Biobank data and showing genetic non-linearity and epistasis.

Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed

The paper identifies HOXB13 as a candidate gene for tail length variation in Merinolandschaf sheep through haplotype mapping and candidate variant analysis.

Mixed ancestry analysis of whole-genome sequencing identifies TBX5 and PTK7 as susceptibility genes for posterior urethral valves

An exploration of linkage fine-mapping on sequences from case-control studies

This paper explores sequence-based linkage analysis for fine-mapping disease traits, showing improved localization compared to genotypic-association methods for rare variants.

Sequencing of over 100,000 individuals identifies multiple genes and rare variants associated with Crohns disease susceptibility

The paper identifies ten new genes with coding variants linked to Crohn's disease risk using sequencing data from over 30,000 patients and 80,000 controls.

A statistical genetics guide to identifying HLA alleles driving complex disease

This paper provides a statistical genetics guide for imputing HLA alleles from genotype data and offers best practices for association testing to identify HLA variants driving complex diseases.

Geographic Confounding in Genome-Wide Association Studies

This study controls for geographic confounding in GWASs of 56 traits, showing that regional differences in SES reduce genetic signals for traits like education and income.

Physiological and behavioural resistance of malaria vectors in rural West-Africa : a data mining study to address their fine-scale spatiotemporal heterogeneity, drivers, and predictability

This study models insecticide resistance and behavioural traits of malaria mosquitoes using environmental and field data to assess their spatial and temporal patterns and drivers.

Strong effects of parasite genotype on drug susceptibility in the Indian subcontinent

The paper assesses the contribution of parasite genotype to drug resistance in Leishmania donovani using heritability and GWAS analyses, finding SNP/indel associations with SSG resistance and copy number variants with MIL resistance.

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

The paper identifies consensus genomic regions associated with multiple abiotic stress tolerance in wheat and suggests their use in breeding for stress resilience.