fine-mapping

Reverse GWAS: Using Genetics to Identify and Model Phenotypic Subtypes

This paper introduces Reverse GWAS (RGWAS) to identify and validate phenotypic subtypes using genetics, finding three novel metabolic subtypes and showing differential treatment effects.

Advantages of genotype imputation with ethnically matched reference panel for rare variant association analyses

This study compares the effectiveness of ethnically matched and mixed reference panels for imputing rare variants in GWAS, showing improved detection of rare variant associations with matched panels.

Sequencing of the MHC region defines HLA-DQA1 as the major independent risk for anti-citrullinated protein antibodies (ACPA)-positive rheumatoid arthritis in Han population

This study identifies HLA-DQA1 as the major independent genetic risk for ACPA-positive RA in Han population through MHC region sequencing and HLA-typing.

Conditional GWAS analysis identifies putative disorder-specific SNPs for psychiatric disorders

This study uses conditional GWAS analysis to identify disorder-specific SNPs for psychiatric disorders, finding some variants with reduced pleiotropy effects.

Probabilistic fine-mapping of transcriptome-wide association studies

This paper introduces a probabilistic framework to fine-map transcriptome-wide association study signals, prioritizing causal genes while accounting for linkage disequilibrium and pleiotropy.

A SIMPLE APPROXIMATION TO THE BIAS IN THE GENETIC EFFECT ESTIMATES WHEN MULTIPLE DISEASE STATES SHARE A CLINICAL DIAGNOSIS

The paper derives a simple approximation to correct genetic effect estimates in case-control GWAS when multiple disease states share a clinical diagnosis and applies it to Alzheimer's disease.

Interrogation of human hematopoiesis at single-cell and single-variant resolution

This study fine-maps genetic variants associated with blood cell traits and identifies cell types and causal mechanisms using single-cell chromatin accessibility data from the UK Biobank.

A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families

Genome-wide association analysis of 350,000 Caucasians from the UK Biobank identifies novel loci for asthma, hay fever and eczema.

This study performs a GWAS on 346,545 UK Biobank participants to identify genetic loci associated with asthma, hay fever, and eczema, finding 141 loci with 41 novel to this study.

Identification of 67 pleiotropic genes for seven autoimmune diseases using multivariate statistical analysis

This study identifies 67 pleiotropic genes shared across seven autoimmune diseases using multivariate analysis and validates their associations with genetic risk.

Recombination within the Cepaea nemoralis supergene is confounded by incomplete penetrance and epistasis

The paper investigates recombination within a supergene in Cepaea nemoralis and finds no evidence of recombination, attributing apparent recombinant phenotypes to incomplete penetrance and epistasis.

Effectiveness of Genomic Selection by Response to Selection for Winter Wheat Variety Improvement

This study evaluates genomic selection effectiveness for winter wheat improvement by assessing prediction accuracy and response to selection across different environmental conditions.

Fine mapping chromatin contacts in capture Hi-C data

The paper introduces a Bayesian method to fine map direct chromatin contacts in capture Hi-C data by identifying a subset of true contacts from apparent long runs of co-contacting fragments.

Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank

This study identifies 64 new genetic signals for osteoarthritis using UK Biobank data, including 52 novel loci, and highlights potential therapeutic targets with existing drugs.

Fine-mapping cis-regulatory variants in diverse human populations

This study fine-maps cis-regulatory variants across diverse human populations by analyzing chromatin accessibility QTLs and their effects on gene expression and long-range interactions.

Leveraging polygenic functional enrichment to improve GWAS power

This paper introduces a method to enhance GWAS power by incorporating functional annotations, resulting in increased detection of genome-wide significant loci.

Leveraging allelic heterogeneity to increase power of association testing

This paper introduces MARS, a statistical method that improves GWAS power by considering multiple causal variants, and shows it identifies more eGenes and association loci than existing methods.

Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

This paper defines ancient ancestry informative markers (aAIMs) and evaluates methods to identify them, showing a PCA-based method outperforms others in classifying ancient Eurasian populations.

Dynamic landscape and genetic regulation of RNA editing in schizophrenia

The paper examines RNA editing changes in schizophrenia by analyzing postmortem brain samples and identifies genetic regulators and associations with schizophrenia GWAS loci.

The genetic basis of mutation rate variation in yeast

This study identifies genetic variants affecting mutation rates in yeast by analyzing natural isolates and segregant progeny, finding heritability and specific genes involved in mutation rate variation.

Identification of 55,000 Replicated DNA Methylation QTL

The paper replicates 55,000 DNA methylation QTLs using two cohorts and finds enrichment of trans mQTLs in specific genomic regions and complex traits.

Discovery Of The First Genome-Wide Significant Risk Loci For ADHD

Genome-wide association meta-analysis of 20,183 ADHD cases and 35,191 controls finds 12 significant loci; signal concentrates in conserved regions, constrained genes, and CNS regulatory elements.

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between kmers and genetic events

DBGWAS is a fast, alignment-free method for bacterial GWAS that identifies interpretable genetic variants associated with phenotypes by analyzing kmer-based subgraphs.

Predicting trait regulators by identifying co-localization of DNA binding and GWAS variants in regulatory regions

CONVERGE identifies co-localization of GWAS variants with transcription factor binding sites in regulatory regions to find novel trait regulators, outperforming existing methods in validating type 2 diabetes regulators.

Genetics of human plasma lipidome: Understanding lipid metabolism and its link to diseases beyond traditional lipids

The paper conducts GWAS and PheWAS on plasma lipid species to identify genetic associations and their links to diseases beyond traditional lipid measures.

Genome wide association study of hippocampal subfield volume in PTSD cases and trauma-exposed controls

The paper conducts a GWAS of hippocampal subfield volumes in PTSD cases and trauma-exposed controls, identifying genetic associations and gene-environment interactions.

A Whole-Genome Association Approach for Large-scaled Inter-species Trait

The paper introduces a whole-genome association approach using kmer frequencies to study large-scale inter-species traits, applying it to chromosome number in mammalian proteomes and identifying candidate genes.

The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits

The paper conducts a GWAS in non-European populations, identifies new genetic loci, and highlights the importance of diverse cohorts for understanding complex traits.

Mapping and Analysis of QTL for Early Maturity Trait in Tetraploid Potato (Solanum tuberosum L.)

The paper maps a QTL for early maturity in tetraploid potato using a segregation population and identifies a 471kb interval containing 34 genes, including PUB14, potentially related to maturity.

Heritability Informed Power Optimization (HIPO) Leads to Enhanced Detection of Genetic Associations Across Multiple Traits

HIPO enhances genetic association detection by optimizing pleiotropic analysis using heritability and trait overlaps, increasing significant loci across multiple traits.