fine-mapping

Fast Bayesian fine-mapping of 35 production, reproduction and body conformation traits with imputed sequences of 27K Holstein bulls

The paper imputes sequence variants in Holstein bulls and performs fine-mapping of 35 traits using a Bayesian approach, identifying candidate genes and variants.

Genome-Wide Association Study Reveals Genetic Link Between Diarrhea-Associated Entamoeba histolytica Infection And Inflammatory Bowel Disease

This study identifies genetic variants associated with Entamoeba histolytica infection and links them to inflammatory bowel disease susceptibility.

Fine-mapping identifies causal variants for RA and T1D in DNASE1L3, SIRPG, MEG3, TNFAIP3 and CD28/CTLA4 loci

This study fine-maps RA and T1D loci outside the MHC, identifying causal variants and confirming their functional impact through allele-specific binding and enhancer activity.

Population history of the Sardinian people inferred from whole-genome sequencing

This study uses whole-genome sequencing of 3,514 Sardinians to explore population history, finding genetic isolation in the Gennargentu region and sex-biased demographic patterns.

Genome-wide association studies on endometriosis and endometriosis-related infertility

This study conducts genome-wide association analyses for endometriosis and endometriosis-related infertility, identifying new candidate loci and replicating known ones.

Genome-Wide Control of Population Structure and Relatedness in Genetic Association Studies via Linear Mixed Models with Orthogonally Partitioned Structure

This paper introduces LMM-OPS, a linear mixed model method that improves calibration and power in genetic association studies with ancestry heterogeneity, demonstrating its effectiveness in a GWAS of white blood cell count in Hispanic/Latino women.

Large-scale genome-wide association meta-analysis of endometriosis reveals 13 novel loci and genetically-associated comorbidity with other pain conditions

This study identifies 13 novel genetic loci associated with endometriosis through a large GWAS meta-analysis and finds genetic links to other pain-related conditions.

Evidence for a potential role of miR-1908-5p and miR-3614-5p in autoimmune disease risk using genome-wide analyses

This study identifies miR-1908-5p and miR-3614-5p as potential regulators of autoimmune disease risk through GWAS and eQTL analyses of immune cell data.

High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability

The paper develops ASMC, a fast method to estimate coalescence times from SNP data, detects selection signals and finds enrichment of disease heritability in regions of background selection.

Multiethnic Meta-analysis Identifies New Loci for Pulmonary Function

This study identifies over 50 new genetic loci associated with pulmonary function through a multiethnic meta-analysis of 90,715 individuals.

High-resolution regulatory maps connect cardiovascular risk variants to disease related pathways

This study connects cardiovascular risk variants to disease-related pathways using high-resolution genomic interaction maps in relevant cell types.

Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies

This paper introduces a new method for detecting marginal epistasis in case-control studies and demonstrates its improved power and type I error control compared to existing approaches.

Genome-wide scan and fine-mapping of rare nonsynonymous associations implicates intracellular lipolysis genes in fat distribution and cardio-metabolic risk

This study identifies rare variant associations with fat distribution and cardio-metabolic risk, implicating intracellular lipolysis genes in these traits.

Estimating Heritability and Genetic Correlation in Case Control Studies Directly and with Summary Statistics

This paper evaluates methods for estimating heritability and genetic correlation in case-control studies, finding that PCGC-s accurately handles non-genetic risk factors and provides unbiased estimates for schizophrenia and bipolar disorder.

Multiplexed targeted resequencing identifies coding and regulatory variation underlying phenotypic extremes of HDL-cholesterol in humans

The paper uses targeted resequencing to identify rare coding and noncoding variants associated with extreme HDL-C levels in humans.

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

The paper uses whole genome sequencing to identify genetic variants associated with plasma lipoprotein(a) levels and finds high heritability and inter-ethnic differences in Lp(a) risk.

MODE for detecting and estimating genetic causal variants

The paper introduces MODE, a method for simultaneous fine-mapping and effect size estimation of genetic causal variants using correlated Gaussian/non-Gaussian random variables.

Software update: Moving the R package sommer to multivariate mixed models for genome-assisted prediction

The sommer R package gains a multivariate solver: several random effects at once, with covariance structures set per effect and between traits, for genome-assisted breeding prediction.

Genotyping by sequencing of 393 Sorghum bicolor BTx623 x IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

This study uses genotyping by sequencing to improve QTL detection sensitivity and resolution in a sorghum RIL population, identifying new syntenic regions and separating QTLs for plant height and flowering time.

Evaluation and application of summary statistic imputation to discover new height-associated loci

This study evaluates summary statistics imputation for discovering new height-associated loci, finding it more effective than genotype imputation in distinguishing true associations from null results.

Burly1 is a mouse QTL for lean body mass that maps to a 0.8-Mb region on chromosome 2

This study fine maps a mouse QTL for lean body mass (Burly1) to a 0.8-Mb region on chromosome 2, showing the B6 allele increases lean body mass without affecting food intake or activity.

Shared genetic contribution to type 1 and type 2 diabetes risk

This study identifies shared genetic risk factors between type 1 and type 2 diabetes, showing overlapping regulatory elements and causal variants affecting islet function and growth.

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

The paper develops a machine learning system using convolutional neural networks to predict cell type-specific epigenetic and transcriptional profiles from DNA sequence, showing alignment with eQTL causal variants.

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

Genome-wide association meta-analysis of 130,664 major depression cases and 330,470 controls identifies 44 independent risk loci enriched in cortical neurons, conserved mammalian regions, splicing networks, and antidepressant targets.

Multiplex Confounding Factor Correction for Genomic Association Mapping with Squared Sparse Linear Mixed Model

This paper introduces a Squared-LMM model to correct confounding factors in genomic association mapping, showing improved accuracy in predicting trait-locus associations using synthetic and real data.

Haplotype sharing provides insights into fine-scale population history and disease in Finland

This study uses haplotype sharing among Finns to reconstruct recent population history and identify regions with increased rare disease variant sharing.

Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits.

The paper compares methods for estimating heritability and genetic architecture using whole genome data and finds that larger imputation panels improve accuracy of causal variant frequency estimates.

Genome-wide association study of depression phenotypes in UK Biobank (n = 322,580) identifies the enrichment of variants in excitatory synaptic pathways

This study conducts a GWAS on depression phenotypes in UK Biobank, identifying genetic variants enriched in excitatory synaptic pathways.

Meta-analysis of genetic association with diagnosed Alzheimer’s disease identifies novel risk loci and implicates Abeta, Tau, immunity and lipid processing

This study performs a large GWAS of Alzheimer's disease, identifies four new risk loci, and highlights pathways involving immunity, lipid metabolism, and APP/Aβ processing.

Refining The Accuracy Of Validated Target Identification Through Coding Variant Fine-Mapping In Type 2 Diabetes

This study identifies 16 causal coding variants in type 2 diabetes using fine-mapping and shows that one third of signals are false leads.