fine-mapping

Sequence based mapping identifies AWNS1, a candidate transcription repressor underlying awn suppression at the B1 locus in wheat

In the presence of population structure: From genomics to candidate genes underlying local adaptation

The paper compares mixed linear models and Spearman correlations for identifying SNPs associated with climate, finding that SNPs from both methods are enriched for local adaptation but only GEMMA-associated SNPs show functional constraint and fitness QTL linkage.

Impact of serum calcium levels on local and total body bone mineral density: A Mendelian randomization study and an age stratum analysis

This study uses Mendelian randomization to show that higher serum calcium levels are associated with reduced bone mineral density in specific age groups and body sites.

Genome-Wide Polygenic Risk Scores and prediction of Gestational Diabetes in South Asian Women

This study develops polygenic risk scores for gestational diabetes in South Asian women using multi-ethnic summary statistics and validates them in UK Biobank data, finding moderate heritability.

Fine mapping using whole-genome sequencing confirms anti Mullerian hormone as a major gene for sex determination in farmed Nile tilapia (Oreochromis niloticus L.)

The paper uses whole-genome sequencing to fine-map sex determination genes in Nile tilapia, identifying anti-Mullerian hormone as a major gene.

Genome-Wide Association Studies of malaria susceptibility and resistance: progress, pitfalls and prospects

This paper reviews progress and challenges in GWAS of malaria susceptibility, highlighting the need for integrative approaches to understand genetic basis of resistance.

Powerful statistical method to detect disease associated genes using publicly available GWAS summary data

The paper introduces a statistical method to detect disease-associated genes using GWAS summary data, identifying novel genes related to beta-cell function and lipid traits.

Pleiotropic Meta-Analysis of Cognition, Education, and Schizophrenia Differentiates Roles of Early Neurodevelopmental and Adult Synaptic Pathways

The paper uses pleiotropic meta-analysis to identify genetic loci associated with cognition, education, and schizophrenia, revealing distinct biological mechanisms for concordant and discordant genetic correlations.

Analytical strategies to include the X-chromosome in variance heterogeneity analyses: evidence for trait-specific polygenic variance structure

The paper investigates X-chromosome variance heterogeneity in quantitative traits using generalized Levene's test and sex-stratified analysis, finding possible polygenic structure for human height variance.

Sharing information between related diseases using Bayesian joint fine mapping increases accuracy and identifies novel associations in six immune mediated diseases

This paper introduces a Bayesian joint fine-mapping method that improves accuracy in identifying causal variants across related immune-mediated diseases by leveraging shared genetic information.

Runs of Homozygosity in sub-Saharan African populations provide insights into a complex demographic and health history

This study analyzes runs of homozygosity in sub-Saharan African populations to uncover demographic history and health-related genetic variation.

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites.

The paper identifies 746k polymorphic sites in Capsicum species and finds four novel loci associated with fruit shape, including a mutation in the Longifolia 1-like gene.

Genetic admixture patterns in Argentinian Patagonia

This study analyzes genetic admixture in Argentinian Patagonia using 46 ancestry informative markers, revealing regional variations in Native American, European, and African ancestry contributions.

GWAS and PheWAS of Red Blood Cell Components in a Northern Nevadan Cohort

This study performs GWAS and PheWAS on red blood cell components in a Northern Nevadan cohort, identifying genetic associations and linking SNPs to phenotypic diagnoses.

Genetic And Epigenetic Fine Mapping Of Complex Trait Associated Loci In The Human Liver

The paper fine-maps 77 GWAS loci in the human liver by integrating epigenetic and gene expression data to understand genetic and epigenetic regulation of gene expression.

Fine scale population structure linked to neutral divergence in the common sole (Solea solea), a marine fish with high dispersal capacity

The paper examines population structure in common sole using ddRAD SNPs, finding that neutral processes, not selection, drive fine-scale divergence in the North Sea-Baltic Sea transition zone.

Bivariate causal mixture model quantifies polygenic overlap between complex traits beyond genetic correlation

MiXeR quantifies polygenic overlap between complex traits using GWAS summary statistics, revealing shared causal variants beyond genetic correlation.

New kinship and FST estimates reveal higher levels of differentiation in the global human population

The paper introduces new kinship and FST estimators, showing higher genetic differentiation in global human populations compared to existing methods.

Ocular disease mechanisms elucidated by genetics of human fetal retinal pigment epithelium gene expression

This study identifies fRPE-specific genes and variants associated with AMD and myopia, revealing novel e/sQTL and mechanisms linking a common variant to both diseases.

Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility

The paper identifies a functional RASGRP1 variant associated with SLE risk through epigenetic and experimental validation, showing it regulates RASGRP1 expression via hnRNP-K binding.

Why high yield QTLs did not succeed in preventing yield stagnation in rice?

This study examines why high-yield QTLs have not prevented rice yield stagnation, finding that they often have low absolute yield and focus on single traits without considering trait trade-offs.

Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci

The paper uses iPSC-derived retinal pigment epithelium to identify and functionally characterize causal variants at AMD risk loci, finding rs943080 as the probable causal variant at VEGFA.

Complex-Traits Genetics Virtual Lab: A community-driven web platform for post-GWAS analyses

A web platform bundling LD-score regression, DEPICT, MetaXcan, SMR, GSMR and fastBAT over uploaded or 1,500-plus public GWAS summary statistics, with precomputed gene, pathway and tissue results.

Genome-wide estimates of heritability and genetic correlations in Essential Tremor

This study estimates heritability and genetic correlations for essential tremor using genome-wide data, finding high heritability and no significant genetic overlap with Parkinson's disease or restless legs syndrome.

Analysis of 100 high coverage genomes from a pedigreed captive baboon colony

The paper analyzes 100 high-coverage genomes from a captive baboon colony to catalog genetic variation, study ancestry, correct colony records, and investigate inbreeding effects.

FunSPU: a versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data

FunSPU is a multiple functional annotation-based association test for WGS data that adapts to annotations and variants, identifying LDL-associated loci missed by existing methods.

GNI-A1 mediates trade-off between grain number and grain weight in tetraploid wheat

This study identifies GNI-A1 as a gene mediating the trade-off between grain number and grain weight in tetraploid wheat through fine-mapping and functional analysis.

Multi-SNP Mediation Intersection-Union Test

The paper introduces SMUT, a method to test mediation effects of multiple SNPs on phenotypes, showing improved power and identifying known mediators in a real dataset.

Beyond power: Multivariate discovery, replication, and interpretation of pleiotropic loci using summary association statistics

This paper develops a multi-trait framework for discovering, replicating, and interpreting pleiotropic loci using GWAS summary statistics, identifying novel genetic associations without additional genotyping.

An integrative analysis of GWAS and intermediate molecular trait data reveals common molecular mechanisms supporting genetic similarity between seemingly unrelated complex traits