fine-mapping

Genome-wide association and HLA region fine-mapping studies identify susceptibility loci for multiple common infections

This study identifies susceptibility loci for multiple common infections through genome-wide association and HLA fine-mapping analyses in over 200,000 individuals.

Linkage disequilibrium dependent architecture of human complex traits reveals action of negative selection

The paper quantifies linkage disequilibrium (LD) dependent architecture of complex traits, finding that low LD SNPs have higher heritability, likely due to negative selection.

Detecting ancient positive selection in humans using extended lineage sorting

This study detects ancient positive selection in humans by identifying genomic regions where Neandertals and Denisovans fall outside present-day human variation, finding evidence for regulatory changes associated with human-specific traits.

A scalable Bayesian method for integrating functional information in genome-wide association studies

This paper introduces a Bayesian method that integrates functional annotations into GWAS to identify causal variants and improve biological interpretation.

Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach

This study uses IIb-RAD sequencing and random forest algorithms to identify SNPs for fine-scale discrimination of Lepeophtheirus salmonis populations in the North-East Atlantic.

Implicating candidate genes at GWAS signals by leveraging topologically associating domains

The paper introduces a method to identify candidate genes at GWAS signals by analyzing gene content within topologically associating domains, demonstrating its application to bone mineral density data.

Estimating inflation in GWAS summary statistics due to variance distortion from cryptic relatedness

The paper estimates residual inflation in GWAS summary statistics caused by cryptic relatedness and shows correction reduces significant loci for height and schizophrenia.

Identity-By-Descent Refines Mapping Of Candidate Regions For Preaxial Polydactyly In A Large Chinese Pedigree

The paper uses identity-by-descent analysis to refine the candidate region for preaxial polydactyly in a Chinese family, identifying two 380 Kb fragments on chromosome 7q36.

Genome Wide Association Analyses Based On Broadly Different Specifications For Prior Distributions, Genomic Windows, And Estimation Methods

This paper compares different prior distributions and genomic window strategies for genome-wide association analysis, finding that heavy-tailed and variable selection priors with adaptive windows perform best.

Constraints on eQTL fine mapping in the presence of multi-site local regulation of gene expression

This study shows that multi-site regulation of gene expression leads to biased eQTL fine mapping and highlights the need for joint multi-site analysis to improve accuracy.

Widespread allelic heterogeneity in complex traits

The paper develops a method to infer allelic heterogeneity in GWAS and eQTL datasets, identifying 4152 loci with strong evidence of AH across different traits.

Co-localization of Conditional eQTL and GWAS Signatures in Schizophrenia

The paper integrates GWAS and conditional eQTL data to identify schizophrenia risk loci with co-localization, finding 40 loci and six with conditional eQTL co-localization.

Type 1 diabetes genome-wide association analysis with imputation identifies five new risk regions

Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection

This study fine-maps genetic loci associated with spontaneous clearance of hepatitis C virus infection, identifying a narrower region in the MHC locus and suggesting subtype-specific effects.

Population Genetic Analysis of the DARC Locus (Duffy) Reveals Adaptation from Standing Variation Associated with Malaria Resistance in Humans

The paper analyzes the DARC locus in humans to show strong selection on the FY*O allele associated with malaria resistance, with a selection coefficient of 5% and a TMRCA of 42 kya.

Integrating Molecular QTL Data into Genome-wide Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization

The paper introduces a Bayesian framework to integrate molecular QTL data into genetic association analysis, assessing enrichment and colocalization of genetic variants.

A fast multi-locus random-SNP-effect EMMA for genome-wide association studies

The paper introduces FASTmrEMMA, a fast multi-locus GWAS method that improves power, model fit, and speed compared to existing approaches.

Fine mapping of Ur-3, a historically important rust resistance locus in common bean

This paper fine maps the Ur-3 rust resistance locus in common bean to a 46.5 Kb region and develops a highly accurate KASP marker, SS68, for marker-assisted selection.

Case-control association mapping without cases

This paper demonstrates genome-wide association studies using family history of disease instead of cases, identifying new risk loci for Alzheimer's, coronary artery disease, and type 2 diabetes.

A complex multi-locus, multi-allelic genetic architecture underlying the long-term selection-response in the Virginia body weight line of chickens

The paper investigates the genetic architecture of long-term selection responses in Virginia chicken lines, identifying multiple loci and genetic mechanisms contributing to body weight variation.

Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

This study uses genome sequencing and epigenomic data to identify genetic variants influencing blood cell traits and uncover regulatory mechanisms in hematopoiesis.

Molecular genetic aetiology of general cognitive function is enriched in evolutionarily conserved regions

This study identifies that genetic variants associated with cognitive function are enriched in evolutionarily conserved regions, which account for a significant portion of heritability.

Scaling probabilistic models of genetic variation to millions of humans

This paper develops TeraStructure, a Bayesian inference algorithm for analyzing large-scale genetic variation data, showing improved speed and accuracy on datasets up to 10K individuals.

Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions

This study introduces iMAAPs, a method to infer multiple-wave population admixture by modeling ALD decay with polynomial functions, showing improved performance over existing methods.

A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification

The paper introduces a new tomato population for high-resolution QTL mapping and gene identification, demonstrating its utility for fine-mapping and epistatic QTL analysis.

Improved methods for multi-trait fine mapping of pleiotropic risk loci

This paper introduces fastPAINTOR, a method that improves fine-mapping accuracy at pleiotropic risk loci by integrating functional annotations and multi-trait data, reducing the number of SNPs needed for follow-up.

Correcting subtle stratification in summary association statistics

This paper introduces PC loading regression to correct population stratification in GWAS summary statistics, showing it reduces LDSC intercept inflation in traits like height and eye color.

Recent advances in the study of fine-scale population structure in humans

This paper reviews recent advances in detecting and understanding fine-scale population structure in humans, highlighting improvements in statistics, computational methods, and haplotypic modeling.

QCAT: testing causality of variants using only summary association statistics

QCAT tests causality of genetic variants using summary association statistics without assuming causal variants are catalogued.

Fast genotyping of known SNPs through approximate k-mer matching

LAVA is a fast and accurate SNP genotyping method using approximate k-mer matching, outperforming existing pipelines in speed and accuracy for dbSNP and Affymetrix SNPs.