fine-mapping

Confirmation and fine mapping of the resistance locus Ren9 from the grapevine cultivar 'Regent'

This study confirms and fine-maps a resistance locus Ren9 in grapevine against powdery mildew, identifying its location and providing genetic markers for marker-assisted selection.

A Framework to Analyse and Interpret Mouse Functional Genome by Prioritizing High Impact SNPs

The paper introduces a computational method to prioritize high-impact SNPs in mouse genomes by linking them to biological functions and pathways, using precomputed annotations and statistical tests.

Genetic Fine-mapping with Dense Linkage Disequilibrium Blocks: genetics of nicotine dependence

This paper introduces a novel ℓ0 graph norm shrinkage algorithm for genetic fine-mapping, demonstrating improved sensitivity and reduced false positives in identifying causal variants for nicotine dependence.

A Powerful Method for Pleiotropic Analysis under Composite Null Hypothesis Identifies Novel Shared Loci Between Type 2 Diabetes and Prostate Cancer

Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease

The paper assesses and improves Mendelian disease-derived pathogenicity scores for common disease using stratified LD score regression and a gradient boosting framework.

Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq

The paper uses snATAC-seq to map chromatin accessibility QTLs in immune cell types and fine-maps complex trait loci, identifying cell type-specific causal variants.

Identity-by-descent detection across 487,409 British samples reveals fine-scale population structure, evolutionary history, and trait associations

The paper detects identity-by-descent segments in 487,409 UK Biobank samples to reveal population structure, evolutionary history, and trait associations.

Functionally-informed fine-mapping and polygenic localization of complex trait heritability

This paper introduces PolyFun, a method that improves fine-mapping accuracy by integrating genome-wide functional data, leading to more causal variant identifications and polygenic localization of trait heritability.

A multi-omic integrative scheme characterizes tissues of action at loci associated with type 2 diabetes

The paper develops a framework to determine tissue-of-action for type 2 diabetes GWAS signals by integrating gene expression and epigenomic data, revealing key tissues and enhancing functional interpretation.

Interactions between two QTLs for time to anthesis on spike development and fertility in wheat

The paper studies the interaction between two QTLs, Eps-7D and Eps-2B, on flowering time and spike fertility in wheat under field conditions, finding their minor but modulated effects and distinct developmental impacts.

Genomic Insights into the Demographic History of Southern Chinese

Genome-wide SNPs from 211 Southern Chinese, analysed with over 1,200 ancient and modern genomes, split the Yangtze River Farmer lineage into four language-linked sub-ancestries and date later migrations.

Antigenic Sensitivity of Membrane-Proximal Targeting Chimeric Antigen Receptors can be Fine-Tuned through Hinge Truncation

This study shows that truncating the CD8 hinge domain in CARs can finely tune antigen sensitivity, improving selectivity for tumor cells over healthy ones.

An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease

The paper introduces a multivariate GWAS framework that identifies functional variants and disease associations by transforming multivariate results into univariate phenotypes for follow-up analysis.

Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum

The paper uses existing trait datasets from a sorghum population to identify pleiotropic loci through multivariate analysis, revealing new insights into phenotypic trade-offs.

LocusFocus: A web-based colocalization tool for the annotation and functional follow-up of GWAS

LocusFocus is a web tool that tests colocalization between GWAS and eQTL data to identify relevant genes and tissues for GWAS loci.

TreeMap: A Structured Approach to Fine Mapping of eQTL Variants

TreeMap identifies causal eQTL variants by accounting for multisite effects and linkage, showing improved accuracy and enabling genome-wide analysis of long-range eQTL.

A new approach of dissecting genetic effects for complex traits

This paper introduces an iterative screen regression (ISR) method for GWAS that improves power and accuracy in detecting genetic associations while correcting for population structure.

nMAGMA: a network enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia

nMAGMA improves risk gene annotation from GWAS summary statistics by integrating regulatory networks and tissue-specific signals, identifying more schizophrenia-related genes than existing methods.

Utility of a high-resolution mouse single nucleotide polymorphism microarray assessed for rodent comparative genomics

The paper assesses the utility of the Mouse Diversity Genotyping Array (MDGA) for cross-species genomic studies in non-model rodents, finding it effective for closely related species but underestimating diversity in more distant ones.

Transcriptome and interactome analyses identify the TP53 interacting gene RCCD1 as a candidate susceptibility gene at the 15p26.1 breast and ovarian cancer risk locus

The paper identifies RCCD1 as a susceptibility gene for breast and ovarian cancer by fine-mapping a risk locus and showing its expression and interaction patterns are associated with cancer risk.

Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty

The paper identifies 31 new genomic risk loci for hearing difficulty using GWAS and multi-omic analysis, highlighting gene regulation in cochlear cells.

Multi-ethnic transcriptome-wide association study of prostate cancer

This study conducts a multi-ethnic GWAS and PrediXcan analysis of prostate cancer, identifying significant gene-tissue pairs and SNPs in African American and Japanese American cohorts.

Intrinsic DNA topology as a prioritization metric in genomic fine-mapping studies

This study introduces DNA topology as a prioritization metric for genomic fine-mapping, using minor groove width changes to identify functionally relevant SNPs in non-coding regions associated with System Lupus Erythematosus.

A response to Yurko et al: H-MAGMA, inheriting a shaky statistical foundation, yields excess false positives

The paper updates H-MAGMA to address statistical issues, showing reduced false positives and consistent results in psychiatric disorder GWAS.

Open Targets Genetics: An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

The paper presents an open resource for fine-mapping and gene prioritization at GWAS loci, identifying causal variants and genes and improving drug target identification.

Delineating the Genetic Component of Gene Expression in Major Depression

This study identifies 91 genes with differential gene expression in major depression using TWAS, including 8 high-confidence causal associations and novel risk genes.

Dutch population structure across space, time and GWAS design

The paper analyzes Dutch population structure using genome-wide data, identifying haplotypic clusters and showing that fine-grained haplotypic covariates reduce GWAS confounding.

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits

Fine-mapping identifies NAD-ME1 as a candidate underlying a major locus controlling temporal variation in primary and specialized metabolism in Arabidopsis

This study identifies NAD-ME1 as a candidate gene underlying a major QTL controlling temporal variation in metabolism and circadian clock outputs in Arabidopsis.

Gene-environment interactions using a Bayesian whole genome regression model

This paper introduces a Bayesian whole genome regression model to analyze gene-environment interactions in the UK Biobank, finding that GxE effects explain a notable proportion of phenotypic variance in several traits.