fine-mapping

Statistical learning for sparser fine-mapped polygenic models: the prediction of LDL-cholesterol

The paper applies statistical learning methods to develop sparser polygenic models for LDL-cholesterol prediction using UK Biobank data, showing competitive performance compared to classical approaches.

An efficient and robust tool for colocalisation: Pair-wise Conditional and Colocalisation (PWCoCo)

PWCoCo improves genetic colocalisation by integrating conditional and colocalisation analyses, enabling robust detection of independent signals and secondary loci in high-dimensional omics data.

Genetics of the human microglia regulome refines Alzheimer's disease risk loci

The paper identifies regulatory mechanisms for 21 Alzheimer's disease risk loci in human microglia using transcriptome and chromatin accessibility profiling.

Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies

This paper introduces MA-FOCUS, a multi-ancestry fine-mapping framework that improves the identification of causal genes in TWAS by leveraging ancestry-specific LD and eQTL patterns.

A cross-disorder dosage sensitivity map of the human genome

This study identifies 114 genome-wide significant rare CNV-disease associations across 30 neurological disorders, revealing 38 novel triplosensitive genes and developing a model to predict dosage sensitivity.

Genome-wide epistasis analysis in Parkinson's disease between populations with different genetic ancestry reveals significant variant-variant interactions

The paper identifies and replicates epistatic variant-variant interactions in Parkinson's disease across genetically diverse populations using a new pipeline called VARI3.

Multi-ancestry GWAS of major depression aids locus discovery, fine-mapping, gene prioritisation, and causal inference

This paper conducts a multi-ancestry GWAS of major depression, identifying 190 loci and 354 genes, with findings showing increased fine-mapping power and bidirectional BMI relationship in European ancestry samples.

Fine-mapping from summary data with the "Sum of Single Effects" model

This paper extends the SuSiE model to work with summary data, showing it is competitive with existing methods in speed and accuracy for fine-mapping genetic variants.

Fine-mapping and comparative genomic analysis reveal the gene composition at the S and Z self-incompatibility loci in grasses

This study fine-maps the Z-locus in perennial ryegrass and identifies two genes encoding DUF247 domain proteins and sZ as pollen and stigma determinants, revealing a duplicated origin of the SI system in grasses.

17q21.31 sub-haplotypes underlying H1-associated risk for Parkinsons disease are associated with LRRC37A/2 expression in astrocytes

The paper identifies three H1 sub-haplotypes at the 17q21.31 locus associated with Parkinson's disease risk and links them to LRRC37A/2 expression in astrocytes.

Multi-trait Analysis of GWAS (MTAG) of Substance Use Traits Identifies Novel Genetic Loci and Phenomic Associations

This paper applies MTAG to GWAS of substance use traits, identifying novel genetic loci and showing improved polygenic risk scores for four disorders.

flashfm-ivis: interactive visualisation for fine-mapping of multiple quantitative traits

flashfm-ivis provides interactive visualizations for exploring shared and distinct causal variants across multiple quantitative traits using fine-mapping results.

Trans-ancestry meta-analysis improves performance of genetic scores for multiple adiposity-related traits in East Asian populations

This paper improves genetic scores for adiposity traits in East Asian populations by using trans-ancestry meta-analysis, increasing variance explained compared to European-derived scores.

Genomic evidence for ancient migration routes along South America's Atlantic coast

The paper analyzes ancient genomes from Northeast Brazil and compares them to other ancient and present-day data, revealing migration routes along South America's Atlantic coast and unexpected ancestry signals.

Admixture mapping screening of CKD traits and risk factors in U.S. Hispanic/Latino individuals from Central America country-of-origin

The paper identifies ancestry-derived loci associated with CKD traits and risk factors in U.S. Hispanic/Latino individuals of Central American origin using admixture mapping.

Leveraging the local genetic structure for trans-ancestry association mapping

This paper introduces LOG-TRAM, a method to improve trans-ancestry association mapping by leveraging local genetic structure, enhancing power and reducing bias in under-represented populations.

Uncertainty Quantification in Variable Selection for Genetic Fine-Mapping using Bayesian Neural Networks

This paper introduces a Bayesian neural network approach for variable selection in genetic fine-mapping, showing improved identification of true effect variables in complex traits.

Genomic stock structure of the marine teleost tarakihi (Nemadactylus macropterus) provides evidence of fine-scale adaptation and a temperature-associated cline amid panmixia

This study uses whole-genome resequencing to analyze tarakihi populations, finding weak genetic differentiation and a temperature-associated genomic cline despite panmixia.

Investigating the genetic architecture of eye colour in a Canadian cohort

This study identifies genetic loci associated with eye colour in a Canadian European cohort, highlighting the HERC2/OCA2 region and other genes, and explores their molecular mechanisms.

ezQTL: A Web Platform for Interactive Visualization and Colocalization of Quantitative Trait Loci and GWAS

ezQTL provides a web tool for colocalizing GWAS and molecular QTL data to identify causal genes and variants.

Age and diet shape the genetic architecture of body weight in Diversity Outbred mice

The paper quantifies diet-dependent genetic contributions to body weight in mice and identifies loci associated with age- and diet-dependent body weight variation.

Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank

The paper identifies two independent asthma-associated loci in the HLA region using exome-wide CNV analysis in UK Biobank, highlighting challenges with CNV detection in complex genomic regions.

An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs

The paper derives an empirical distance cutoff to distinguish cis and trans protein QTLs using a large-scale pQTL study and applies it to molecular GWAS traits.

Shared components of heritability across genetically correlated traits

This paper introduces PDR to identify shared heritability components across genetically correlated traits and validates it on coronary disease, asthma, and type II diabetes traits.

The Genomic Prehistory of the Indigenous People of Uruguay

This study presents the first whole genome sequences of pre-European contact Indigenous people from Uruguay, revealing connections to ancient Panama and eastern Brazil but not modern Amazonians, suggesting a distinct Atlantic coastal migration route.

Mapping genomic loci prioritises genes and implicates synaptic biology in schizophrenia

A genome-wide association study of 69,369 schizophrenia cases and 236,642 controls identifies 270 risk loci, prioritizes 130 genes, and links common and rare risk variants to neuronal synaptic biology.

A Genome-Wide Association Analysis of Happiness: Consistent Genetic Effects Across the Lifespan and Across Genetic Ancestries in Multiple Cohorts.

This paper conducts a genome-wide association study of happiness, identifying genetic loci and correlations with personality traits, and shows consistent genetic effects across age and ancestry.

Leveraging fine-mapping and non-European training data to improve cross-population polygenic risk scores

This paper introduces PolyPred and PolyPred+ to improve cross-population polygenic risk score accuracy by addressing LD, MAF, and causal effect size differences using fine-mapping and non-European training data.

Newfoundland and Labrador: A mosaic founder population of an Irish and British diaspora from 300 years ago.

This study analyzes the genetic structure of Newfoundland and Labrador using SNP data, revealing coastal community clustering, religious denomination associations, and a recent population bottleneck.

High-density mapping of QTL controlling agronomically important traits in quinoa (Chenopodium quinoa Willd.)

This study constructs a high-density genetic map of quinoa using Skim-seq and identifies fifteen QTL for ten agronomically important traits, including pleiotropic loci for flowering time and plant height.