fine-mapping

Genetic drift from the out-of-Africa bottleneck leads to biased estimation of genetic architecture and selection

The paper shows that genetic drift from the Out-of-Africa bottleneck biases the estimation of genetic architecture and selection, and proposes a model to correct for this bias.

Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes

The paper introduces POLMM, a mixed model for ordinal categorical phenotypes in GWAS, showing it is computationally efficient, controls type I error, and identifies more significant variants than existing methods.

Genetic-substructure and complex demographic history of South African Bantu speakers

This study investigates genetic substructure and demographic history of South African Bantu speakers using genome-wide data, revealing fine-scale population structure aligned with geography and linguistics.

Discovery and fine-mapping of kidney function loci in first genome-wide association study in Africans

This study conducts the first GWAS of eGFR in Africans, identifies two genome-wide significant loci, and highlights the need for more African-specific genetic research on kidney function.

Fine-scale population structure reveals high genetic heterogeneity of the Kuwaiti population in the Arabian Peninsula

This study identifies high genetic heterogeneity in the Kuwaiti population by analyzing genome-wide SNP data from 583 individuals, revealing distinct subgroups with different ancestral origins.

Significance testing for small annotations in stratified LD-Score regression

The paper shows that S-LDSC's significance testing fails for small annotations, leading to inflated type 1 error, and proposes thresholds to control this error.

A multi-task convolutional deep learning method for HLA allelic imputation and its application to trans-ethnic MHC fine-mapping of type 1 diabetes

DEEP*HLA improves HLA allelic imputation for low-frequency alleles, enabling trans-ethnic MHC fine-mapping of type 1 diabetes with high accuracy.

In silico candidate variant and gene identification using inbred mouse strains

The paper introduces MouseFM, a tool for in silico fine-mapping of genetic variants and genes using inbred mouse strain data, and demonstrates its application to identify candidate variants for specific phenotypes.

Genetic correlates of socio-economic status influence the pattern of shared heritability across mental health traits

The paper investigates how genetic correlates of socio-economic status affect shared heritability across mental health traits using genome-wide association summary statistics.

Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS

The paper introduces CC-GWAS, a method to detect allele frequency differences among cases of psychiatric disorders using summary statistics, identifying 196 loci distinguishing eight disorders.

Scalable unified framework of total and allele-specific counts for cis-QTL, fine-mapping, and prediction

The paper introduces a scalable framework integrating total and allele-specific gene expression to improve detection of genetic effects on gene expression, showing a 29% power gain equivalent to increased sample size.

Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations

This study develops a computational pipeline to reconstruct genomes from ultra-low coverage data in Hybrid Swarm populations and evaluates its effectiveness for genetic association studies.

Admixture/fine-mapping in Brazilians reveals a West African associated potential regulatory variant (rs114066381) with a strong female-specific effect on body mass- and fat mass-indexes

The paper identifies a West African-associated regulatory variant with a strong female-specific effect on BMI and fat mass in Brazilian admixed populations.

A large-scale transcriptome-wide association study (TWAS) of ten blood cell phenotypes reveals complexities of TWAS fine-mapping

This paper performs a large-scale TWAS of blood cell phenotypes, identifies 239 gene-trait associations, and develops an R Shiny app to visualize TWAS results.

Prioritization of osteoporosis-associated GWAS SNPs using epigenomics and transcriptomics

This study identifies 16 novel regulatory SNPs associated with osteoporosis risk by integrating epigenomic and transcriptomic data from GWAS.

eMAGMA: An eQTL-informed method to identify risk genes using genome-wide association study summary statistics

eMAGMA converts SNP-level GWAS summary statistics into gene-level associations using tissue-specific eQTL data, outperforming existing methods in identifying causal genes for complex diseases.

Zooming into the genomic vicinity of the major locus for vicine and convicine in faba bean (Vicia faba L.)

This paper identifies a candidate gene for the major locus controlling vicine and convicine levels in faba bean and develops SNP markers for low-VC breeding.

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

This study performs GWAS on three molecular traits, identifying core genes and pathways while highlighting a polygenic background contributing to trait variance.

Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer's disease risk genes

Meta-analysing UK Biobank family-history GWAS with diagnosed-AD GWAS yields 37 loci, four novel (NCK2, TSPAN14, SPRED2, CCDC6); fine-mapping, colocalisation and network scoring prioritize causal genes.

M-GWAS for the gut microbiome in Chinese adults illuminates on complex diseases

This paper performs M-GWAS on a Chinese cohort to identify genetic contributions to the gut microbiome and its associations with complex diseases.

Polygenic risk modeling with latent trait-related genetic components

This paper introduces a latent factor model for polygenic risk scores that decomposes genetic risk into interpretable components, showing improved interpretability over standard PRS for traits like BMI and myocardial infarction.

Coupled Mixed Model for Joint Genetic Analysis of Complex Disorders with Two Independently Collected Data Sets

This paper introduces a method to jointly analyze two independent GWAS datasets with different phenotypes, addressing confounding factors and showing its utility in studying Alzheimer's disease and substance use disorder.

A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits

This paper introduces HyPrColoc, a Bayesian algorithm for multi-trait colocalization using GWAS summary statistics, identifying 43 regions where coronary heart disease colocalizes with other traits.

The PAX1 locus at 20p11 is a modifier for bilateral cleft lip only

The paper investigates genetic differences between bilateral and unilateral cleft lip and palate subtypes using genome-wide association studies and finds distinct genetic architectures.

Genetic analysis of mitochondrial DNA copy number and associated traits identifies loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation, and reveals a causal association of mitochondrial function with mortality

This study identifies 100 loci associated with mitochondrial DNA copy number and finds causal links between mitochondrial function and mortality.

Treatment of the X chromosome in mapping multiple quantitative trait loci

The paper extends a penalized likelihood method for multiple-QTL analysis to handle the X chromosome appropriately, demonstrating its performance through simulation and eQTL data.

Fine-scale Population Structure of North American Arabidopsis thaliana Reveals Multiple Sources of Introduction from Across Eurasia

This study identifies multiple introduction sources of North American Arabidopsis thaliana from Eurasia using genomic data and finds evidence of admixture increasing haplotype diversity and immune-related selection.

Evolutionary dynamics of indels in SARS-CoV-2 spike glycoprotein

The paper analyzes SARS-CoV-2 spike glycoprotein sequences to show that indels are common and increasing, with implications for viral evolution and vaccine efficacy.

Investigating the Genetic Architecture of Non-Cognitive Skills Using GWAS-by-Subtraction

This study identifies 157 genome-wide significant loci associated with non-cognitive contributions to educational attainment, explaining 57% of genetic variance.

H-MAGMA, inheriting a shaky statistical foundation, yields excess false positives

The paper critiques H-MAGMA's statistical foundation, showing many of its findings for psychiatric disorders do not replicate when methodological flaws are addressed.