fine-mapping

Identification and Functional Characterization of Regulatory Variants in DPP9 Associated with COVID-19 Severity

The paper identifies and functionally characterizes regulatory variants in DPP9 associated with severe COVID-19 by analyzing genetic risk factors and their impact on gene expression and immune cell function.

CATaN maps gene regulatory programs that shape genetic risk across complex diseases

CATaN integrates TF-GRNs and transcriptomes to identify genetic risk components across complex diseases, finding 588 significant CC components enriched for SNP heritability.

Multi-ancestry modeling improves fine-mapping resolution, protein prediction, and discovery for proteome-wide association studies

This study improves proteome-wide association study results by using multi-ancestry data, finding more protein-phenotype associations and better prediction models.

Genetic drivers of etiologic heterogeneity in thyroid cancer

This study identifies 51 genetic loci associated with thyroid cancer through a multi-ancestry GWAS and explores pleiotropic relationships to uncover mechanistic clusters and genetic subtypes.

Inferring fine-scale rates of mutation and recombination in the coppery titi monkey (Plecturocebus cupreus)

The paper infers fine-scale mutation and recombination rates in the coppery titi monkey using divergence and polymorphism data and a high-quality genome, aligning with rates in other primates.

Multiple instance fine-mapping: predicting causal regulatory variants with a deep sequence model

The paper introduces MIFM, a deep learning method to predict causal regulatory variants from GWAS data using weak labels and DNA sequences, improving cross-ancestry risk prediction and variant disentanglement.

A cryptic local genetic cluster in Northern France amid the European mosaic of flat oyster lineages revealed by integrating SNP array and whole-genome sequencing

Genetic Association of Somatic Incompatibility and NLR-like Protein Domains in Coprinopsis cinerea

The paper identifies a genetic locus, somA, responsible for allorecognition in Coprinopsis cinerea, revealing a novel mechanism for fungal nonself recognition through polymorphic alleles and purifying selection on an LRR-encoding protein.

Fine mapping of HLA effects in Oral and non-Oral lichen planus

This paper performs fine-mapping of HLA effects in lichen planus subtypes, identifying specific HLA haplotypes associated with increased or decreased risk in oral and non-oral forms.

Fine mapping of PTSD GWAS reveals a role for amygdala Foxp2 in regulation of fear and threat responses

This study fine-maps PTSD GWAS data with amygdala eQTLs and shows FOXP2 expression is linked to increased PTSD risk, with functional validation in mice and humans.

Dissecting the genetic architecture of knee alignment reveals its contribution to osteoarthritis risk

This study identifies 20 genetic loci associated with knee alignment and shows genetic correlation with knee osteoarthritis, suggesting osteoarthritis may causally influence alignment.

Type 2 diabetes genetics in 125,000 admixed adults from Mexico City

This study identifies 86 T2D GWAS associations in 125,000 admixed Mexican adults, including 21 novel signals, and highlights the role of common regulatory variation in the endocrine pancreas.

Quantitative trait loci mapping of gene expression and chromatin accessibility in primary fibroblast reveals shared allelic effects between Latin American and European ancestries

The paper maps gene expression and chromatin accessibility QTLs in fibroblasts from European and Latin American ancestries, finding high concordance and shared regulatory mechanisms.

Selection-guided discovery in South Asians implicates the MAPT locus in insulin resistance

The paper integrates positive selection signatures with genetic data to identify metabolically relevant loci in South Asians, finding the MAPT locus associated with insulin resistance.

Sex differences in PRDM9-independent fine-scale recombination patterns

This study shows that fine-scale recombination patterns are similar between sexes in dogs and barn owls, but male-biased recombination occurs in gene promoters.

Disentangling adiposity-related and non-adiposity-related genetic pathways for type 2 diabetes

This paper identifies 29 circulating proteins associated with type 2 diabetes risk independent of BMI using GWAS-by-subtraction, proteome-wide Mendelian randomization, and colocalization analyses.

Long-term population decline and recombination heterogeneity shape genomic diversity in the American alligator

The paper quantifies genomic diversity in American alligators, finding low nucleotide diversity and structured recombination rates shaped by long-term population history.

Fine-mapping candidate neuropsychiatric regulatory variants using cell type-aware comparative genomics

The paper introduces CTACIT to fine-map neuropsychiatric regulatory variants by integrating conservation scores with cell type-specific open chromatin data across species.

Sex chromosome-aware GWAS reveals XY-linked agronomic architecture and breeding targets in cannabis

This study performs a sex chromosome-aware GWAS on cannabis, identifying 16 genome-wide significant markers on ChrX and ChrY that influence agronomic traits.

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

This paper creates a detailed heart atlas using multimodal data to identify cell states and disease-associated genetic variants in specific heart regions.

A Multi-Context Regulome-Wide Association Atlas for Genetic Studies of Aging Brain Disorders

This paper introduces FGMB, a multi-context regulome-wide association atlas, and applies it to Alzheimer's disease to identify 327 regulatory associations and resolve 86 gene-molecular-trait pairs.

Faroese Whole Genomes Provide Insight into Ancestry and Recent Selection

This study analyzes whole genome sequencing data from the Faroe Islands to explore ancestry, genetic diversity, and signals of recent selection in a North Atlantic founder population.

Relational biological structure improves fine-mapping of causal GWAS variants under weak signal

This paper introduces GAFM and HBP methods to improve GWAS fine-mapping by leveraging biological structure, achieving higher accuracy and speed across multiple species and datasets.

Deconvolution-based cell-type specific DNA methylation-wide and transcriptome-wide association studies identify risk CpG sites and genes associated with colorectal cancer risk

The paper uses deconvolution to identify cell-type-specific DNA methylation and gene expression associations with colorectal cancer risk, finding 178 CpG sites and 68 genes across 26 new loci.

Distinct and shared genetics of kidney filtration function versus albuminuria revealed by multi-trait GWAS

This study performs a multi-trait GWAS on kidney filtration function and albuminuria, identifying distinct genetic signals and shared mechanisms.

Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle

The paper uses long-read RNA-seq to uncover isoform-level and context-specific regulatory effects in cattle, improving the resolution of molecular atlases and GWAS loci.

Genomic Informational Field Theory (GIFT) to identify genetic associations of a complex trait using a small sample size

This paper introduces GIFT, a method that enables accurate genetic association analysis in small datasets, identifying loci linked to height at withers in ponies and validating a hypothesis about insulin physiology.

Positive-control Mendelian randomization highlights power constraints in disease-mortality GWAS

The paper uses Mendelian randomization to show that current disease-mortality GWAS may lack sufficient power to detect shared genetic effects, despite strong associations in case-control studies.

A pilot genome-wide association and gene-level prioritization analysis of ischemic heart disease with co-occurring arterial hypertension in a Kazakh cohort

This paper conducts a GWAS of ischemic heart disease with arterial hypertension in a Kazakh cohort, finding no significant SNPs but prioritizing candidate genes using MAGMA and KGWAS methods.

Comparing fine-scale mutation and recombination landscapes in rhesus macaque (Macaca mulatta) populations of Chinese and Indian descent inferred from both short- and long-read sequencing data

This study compares mutation and recombination landscapes in rhesus macaques from Chinese and Indian populations using short- and long-read sequencing data, revealing population-specific recombination hotspots.