fine-mapping

Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants

The paper uses MPRA to identify functional regulatory variants associated with schizophrenia and shows they differ from eQTLs in genomic location and regulatory impact.

Partitioning heritability using single-cell multi-omics identifies a novel macrophage subpopulation conveying genetic risks of coronary artery disease.

The paper identifies a novel macrophage subpopulation, lipid-handling macrophages, that is enriched with CAD genetic risk and shows how a risk variant affects FDX1 through AP-1 and C/EBP-beta recruitment.

Joint modelling of whole genome sequence data for human height via approximate message passing

This paper introduces gVAMP, an algorithm for analyzing whole genome sequence data to identify genetic variants associated with complex traits like height, showing improved accuracy over existing methods.

Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects

The paper identifies structural variations in whole-genome sequencing data from 16,905 ADSP subjects and finds associations with Alzheimer's disease and related endophenotypes.

Retracing Human Genetic Histories and Natural Selection Using Precise Local Ancestry Inference

Orchestra improves local ancestry inference, revealing admixture patterns in Latin Americans, Ashkenazi Jews, and selection signals in British populations.

Integration of genetic fine-mapping and multi-omics data reveals candidate effector genes for hypertension

The paper integrates genetic fine-mapping with multi-omics data to identify candidate effector genes and new drug targets for hypertension.

Metabolomic-genomic prediction drastically improves prediction accuracy of breeding values in crop breeding

The paper integrates genomic and metabolomic data to improve breeding value prediction for malting quality traits in barley, showing higher accuracy with the metabolomics-genomic model.

Identification of Novel Genomic Loci for Anxiety and Extensive Genetic Overlap with Psychiatric Disorders

This study identifies 114 novel genomic loci for anxiety and finds extensive genetic overlap with schizophrenia, bipolar disorder, major depression, and ADHD.

Evaluation of Bayesian Linear Regression Models as a Fine Mapping tool

This paper evaluates Bayesian Linear Regression models with BayesC and BayesR priors as fine mapping tools, comparing them to existing methods and showing improved F1 scores and credible set properties.

A Multivariate Approach to Understanding the Genetic Overlap between Externalizing Phenotypes and Substance Use Disorders

This study uses Genomic Structural Equation Modeling to identify a common genetic factor underlying externalizing phenotypes and substance use disorders, finding that a single dimension of genetic risk best explains their relationships.

Single-cell genomics improves the discovery of risk variants and genes of Atrial Fibrillation

This study integrates single-cell epigenomics with GWAS to identify risk variants and genes for Atrial Fibrillation, highlighting key transcription factors and pathways.

Nuclear genetic control of mtDNA copy number and heteroplasmy in humans

Blood whole genomes from 274,832 people yield 92 independent nuclear signals for mtDNA copy number and 42 for inherited heteroplasmy levels, implicating mtDNA replication machinery.

Leveraging fine-scale population structure reveals conservation in genetic effect sizes between human populations across a range of human phenotypes

The paper shows genetic effect sizes are similar across African and European populations for most traits, suggesting shared causal mutations and improving GWAS portability.

New machine learning method identifies subtle fine-scale genetic stratification in diverse populations

This paper introduces ALFDA, a machine learning method that improves identification of fine-scale genetic structure and preserves geogenetic distances better than existing methods.

Differences in pathogenetic mechanism between Tibetan and Han high-altitude polycythemia based on a whole genome-wide association study

This study identifies genetic differences in HAPC susceptibility between Tibetans and Han Chinese using GWAS, revealing distinct pathways involved in each group.

Estimating the Genetic Contribution to Astigmatism and Myopia in the Mexican population

This study estimates the genetic contribution to astigmatism and myopia in the Mexican population using twin data and finds high heritability and genetic correlations.

Distinguishing Happiness and Meaning in Life from Depressive Symptoms: a GWAS-by-subtraction study in the UK Biobank

This study uses GWAS-by-subtraction to identify genetic variants specific to happiness and meaning in life independent of depressive symptoms in the UK Biobank.

Genome-wide Association Clustering Meta-analysis in European and Chinese Datasets for Systemic Lupus Erythematosus identifies new genes

This paper applies a locus-based test called OASIS to GWAS datasets from European and Chinese populations to identify 35 common non-HLA SLE genes and their associated pathways.

Functional Genomics in Human iPSC-Derived Sinoatrial Node Cells Reveals Shared Regulatory Determinants of Heart Rate and Atrial Fibrillation

The paper develops a human iPSC-derived sinoatrial node system to study heart rhythm-associated SNPs and identifies causal variants linked to heart rate and atrial fibrillation.

Identification of 64 new risk loci for major depression, refinement of the genetic architecture and risk prediction of recurrence and comorbidities

This study identifies 64 new risk loci for major depression, refines its genetic architecture, and shows strong genetic overlap with other psychiatric disorders and educational attainment.

Genetic fine-mapping from summary data using a non-local prior improves detection of multiple causal variants

This paper introduces FiniMOM, a Bayesian fine-mapping method that improves detection of multiple causal variants using non-local priors and summary data from GWAS.

SR-TWAS: Leveraging Multiple Reference Panels to Improve TWAS Power by Ensemble Machine Learning

SR-TWAS improves TWAS power by combining multiple reference panels and regression methods through ensemble learning, identifying risk genes for Alzheimer's and Parkinson's diseases.

Genetic insights into ossification of the posterior longitudinal ligament of the spine

This study identifies genetic loci and causal traits associated with ossification of the posterior longitudinal ligament of the spine using GWAS and Mendelian randomization analyses.

Does the seed fall far from the tree? Weak fine scale genetic structure in a continuous Scots pine population

The paper examines fine-scale genetic structure in Scots pine, finding low average relatedness at short distances and no site differentiation.

Similarity and diversity of genetic architecture for complex traits between East Asian and European populations

The paper evaluates genetic architecture similarity and diversity between East Asian and European populations for 37 traits using summary statistics, finding shared genetic overlap but also population-specific effects.

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

Flexibly encoded genome-wide association study identifies novel nonadditive genetic risk variants for cardiometabolic traits

This paper introduces EDGE, a method to detect nonadditive genetic effects in GWAS, finding nonadditive patterns in over 52% of significant loci for coronary artery disease and body mass index.

Mapping interindividual dynamics of innate immune response at single-cell resolution

The paper develops GASPACHO to identify dynamic eQTLs in antiviral responses using single-cell RNA-seq, uncovering thousands of eQTLs and linking them to disease risk loci.

Colocalization of blood cell traits GWAS associations and variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variants

The paper identifies 69 blood cell trait GWAS loci potentially driven by PU.1 occupancy variation and nominates 51 variants as causal through colocalization analysis with PU.1 bQTLs.

Multi-ancestry meta-analysis and fine-mapping in Alzheimer's Disease

This study conducts a multi-ancestry GWAS meta-analysis of Alzheimer's disease, identifies two novel loci, and assesses polygenic risk score generalizability across populations.