Detecting latent interaction effects when analyzing binary traits.

In genome-wide association studies (GWAS), it is often desirable to test for interactions, such as gene-environment (G x E) or gene-gene (G x G) interactions, between single-nucleotide polymorphisms (SNPs, G's) and environmental variables (E's). However, directly accounting for interaction is often infeasible, because the interacting variable is latent or the computational burden is too large. For quantitative traits (Y) that are approximately normally distributed, it has been shown that indirect testing on GxE can be done by testing for heteroskedasticity of Y between genotypes.

Increased skin autofluorescence predicts future cancer development.

Tissue glycation, assessed through skin autofluorescence (SAF) using an AGE reader, is linked to an increased risk of type 2 diabetes (T2D), cardiovascular disease (CVD), as well as mortality from both CVD and cancer. It was also suggested that higher SAF be linked to a greater incidence of cancer. We aimed to evaluate the relationship between SAF and the time to a new cancer diagnosis in the Lifelines Cohort Study, a population-based study in the Northern Netherlands, in participants with and without T2D.

Estimating effects of serum vitamin B12 levels on psychiatric disorders and cognitive impairment: a Mendelian randomization study.

Background: Vitamin B12 deficiency can lead to pernicious anemia and has been associated with various neuropsychiatric diseases and cognitive decline. However, it is unclear whether increasing serum vitamin B12 levels can help to prevent the onset of psychiatric disorders and cognitive impairment in the general population.

Methods: Leveraging large-scale genome-wide association studies (GWASs), we conducted Mendelian randomization (MR) and sensitivity analyses to estimate the potential effects of serum vitamin B12 levels on eight psychiatric disorders, educational attainment and cognitive performance.

Genetics of Childhood-onset Systemic Lupus Erythematosus (cSLE).

Objectives: Genome wide association studies (GWAS) have identified >100 loci for systemic lupus erythematosus (SLE). These loci may also impact age of diagnosis. We aimed to identify genetic variants for age of SLE diagnosis, and to complete a GWAS of childhood-onset SLE (cSLE) diagnosed <18 years of age.

Disease-modifying effects of TMEM106B in genetic frontotemporal dementia: a longitudinal GENFI study.

Common variants within TMEM106B are associated with risk for frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP). The G allele of the top single nucleotide polymorphism, rs1990622, confers protection against FTLD-TDP, including genetic cases due to GRN mutations or C9orf72 hexanucleotide repeat expansions. However, the effects of interaction between TMEM106B-rs1990622 and frontotemporal dementia (FTD) mutations on disease endophenotypes in genetic FTD are unknown.

RegionScan: a comprehensive R package for region-level genome-wide association testing with integration and visualization of multiple-variant and single-variant hypothesis testing.

Summary: RegionScan is designed for scalable genome-wide association testing of both multiple-variant and single-variant region-level statistics, with visualization of the results. For detection of association under various regional architectures, it implements three classes of state-of-the-art region-level tests, including multiple-variant linear/logistic regression (with and without dimension reduction), a variance-component score test, and region-level min tests. RegionScan also supports the analysis of multi-allelic variants and unbalanced binary phenotypes and is compatible with widely used variant call format (VCF) files for both genotyped and imputed variants.

Correction: Canadian COVID-19 host genetics cohort replicates known severity associations.

[This corrects the article DOI: 10.1371/journal.pgen.

Dimension Reduction Using Local Principal Components for Regression-Based Multi-SNP Analysis in 1000 Genomes and the Canadian Longitudinal Study on Aging (CLSA).

For genetic association analysis based on multiple SNP regression of genotypes obtained by dense DNA sequencing or array data imputation, multi-collinearity can be a severe issue causing failure to fit the regression model. In this study, we propose a method of Dimension Reduction using Local Principal Components (DRLPC) which aims to resolve multi-collinearity by removing SNPs under the assumption that the remaining SNPs can capture the effect of a removed SNP due to high linear dependency. This approach to dimension reduction is expected to improve the power of regression-based statistical tests.

Characterization of gene-environment interactions for vitamin D through variance quantitative trait loci: a UK Biobank-based genetic epidemiology study.

Background: Understanding gene-environment interactions associated with vitamin D status may refine nutrition and public health strategies for vitamin D deficiency. Recent methodological advances have enabled the identification of variance quantitative trait loci (vQTLs) where gene-environment interactions are enriched.

Objectives: The study aims to identify vQTLs for serum 25-hydroxy vitamin D (25OHD) concentrations and characterize potential gene-environment interactions of vQTLs.

Integrative Proteogenomic Analyses Provide Novel Interpretations of Type 1 Diabetes Risk Loci Through Circulating Proteins.

Identification of circulating proteins that may play a role in the pathogenesis of type 1 diabetes can provide promising targets for biomarker and drug target identification. Supported by multiple lines of evidence, circulating abundances of CTSH, IL27RA, SIRPG, and PGM1 were associated with the risk of type 1 diabetes. Tissues and cell types with enrichment of target protein-coding gene expression were identified.

Genetics of C-Peptide and Age at Diagnosis in Type 1 Diabetes.

Identified genetic loci for C-peptide and type 1 diabetes (T1D) age at diagnosis (AAD) explain only a small proportion of their variation. We aimed to identify additional genetic loci associated with C-peptide and AAD. Some HLA allele/haplotypes associated with T1D also contributed to variability of C-peptide and AAD, whereas outside the HLA region, T1D loci were mostly not associated with C-peptide or AAD.

Autosomal-dominant macular dystrophy linked to a chromosome 17 tandem duplication.

Hereditary macular dystrophies (HMDs) are a genetically diverse group of disorders that cause central vision loss due to photoreceptor and retinal pigment epithelium (RPE) damage. We investigated a family with a presumed novel autosomal-dominant HMD characterized by faint, hypopigmented RPE changes involving the central retina. Genome and RNA sequencing identified the disease-causing variant to be a 560 kb tandem duplication on chromosome 17 [NC_000017.

Skin autofluorescence and cause-specific mortality in a population-based cohort.

We aimed to assess the association of SAF with cardiovascular mortality in the general population and the possible association between SAF with other disease-specific mortality rates. We evaluated 77,143 participants without known diabetes or cardiovascular disease. The cause of death was ascertained by the municipality database.

Association of Genetically Predicted Skipping of COL4A4 Exon 27 with Hematuria and Albuminuria.

Key Points: Using transcriptome-wide association studies, we identified an association between splicing out of exon 27 of COL4A4 and hematuria. We confirmed the presence of COL4A4 exon 27 splicing in an independent cohort. Functional assays revealed that the COL4A4 transcript with exon 27 spliced out affects collagen IV trimer assembly and secretion.

Better together against genetic heterogeneity: A sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank.

Genetic effects can be sex-specific, particularly for traits such as testosterone, a sex hormone. While sex-stratified analysis provides easily interpretable sex-specific effect size estimates, the presence of sex-differences in SNP effect implies a SNP×sex interaction. This suggests the usage of the often overlooked joint test, testing for an SNP's main and SNP×sex interaction effects simultaneously.

Canadian COVID-19 host genetics cohort replicates known severity associations.

The HostSeq initiative recruited 10,059 Canadians infected with SARS-CoV-2 between March 2020 and March 2023, obtained clinical information on their disease experience and whole genome sequenced (WGS) their DNA. We analyzed the WGS data for genetic contributors to severe COVID-19 (considering 3,499 hospitalized cases and 4,975 non-hospitalized after quality control). We investigated the evidence for replication of loci reported by the International Host Genetics Initiative (HGI); analyzed the X chromosome; conducted rare variant gene-based analysis and polygenic risk score testing.

Statistical Learning of Large-Scale Genetic Data: How to Run a Genome-Wide Association Study of Gene-Expression Data Using the 1000 Genomes Project Data.

Teaching statistics through engaging applications to contemporary large-scale datasets is essential to attracting students to the field. To this end, we developed a hands-on, week-long workshop for senior high-school or junior undergraduate students, without prior knowledge in statistical genetics but with some basic knowledge in data science, to conduct their own genome-wide association study (GWAS). The GWAS was performed for open source gene expression data, using publicly available human genetics data.

Analyses of potential causal contributors to increased waist/hip ratio-associated cardiometabolic disease: A combined and sex-stratified Mendelian randomization study.

Background: Increased waist/hip ratio (WHR) contributes to type 2 diabetes, fatty liver, dyslipidaemia, hypertension and coronary artery disease, with potential sex-differential effects. Postulated mediators include increased lipid flux, branched-chain amino acids, glycine and glycoprotein acetyl, but their relative contributions and sex-specific impact on WHR-associated cardiometabolic disease (CMD) are not established.

Methods: We therefore undertook combined and sex-stratified Mendelian randomization (MR) to assess the relative causal contributions of these mediators to WHR-associated CMD using summary statistics from the largest genome-wide association studies in European ancestries.

A genome-wide association, polygenic risk score and sex study on opioid use disorder treatment outcomes.

Opioid use disorder continues to be a health concern with a high rate of opioid related deaths occurring worldwide. Medication Assisted Treatments (MAT) have been shown to reduce opioid withdrawal, cravings and opioid use, however variability exists in individual's treatment outcomes. Sex-specific differences have been reported in opioid use patterns, polysubstance use and health and social functioning.

Comprehensive whole-genome analyses of the UK Biobank reveal significant sex differences in both genotype missingness and allele frequency on the X chromosome.

The UK Biobank is the most used dataset for genome-wide association studies (GWAS). GWAS of sex, essentially sex differences in minor allele frequencies (sdMAF), has identified autosomal SNPs with significant sdMAF, including in the UK Biobank, but the X chromosome was excluded. Our recent report identified multiple regions on the X chromosome with significant sdMAF, using short-read sequencing of other datasets.

Erythritol as a Potential Causal Contributor to Cardiometabolic Disease: A Mendelian Randomization Study.

People with type 2 diabetes frequently use low-calorie sweeteners to manage glycemia and reduce caloric intake. Use of erythritol, a low-calorie sweetener, has increased recently. Higher circulating concentration associates with major cardiac events and metabolic disease in observational data, prompting some concern.

GWAS for the composite traits of hematuria and albuminuria.

Our GWAS of hematuria in the UK Biobank identified 6 loci, some of which overlap with loci for albuminuria suggesting pleiotropy. Since clinical syndromes are often defined by combinations of traits, generating a combined phenotype can improve power to detect loci influencing multiple characteristics. Thus the composite trait of hematuria and albuminuria was chosen to enrich for glomerular pathologies.