Frontiers in Genetics

STUDY QUESTION[Do structural genomic variants, that can be identified by using optical genome mapping, contribute to male infertility?] SUMMARY ANSWER[By using optical genome mapping we can identify several types of structural variants, both known and new, that may contribute to male infertility.] WHAT IS KNOWN ALREADY[Traditional approaches such as karyotyping, CFTR and chromosome Y microdeletion testing are successful in explaining clinical findings in [~]30% of MI patients, leaving the rest...

Study questionDo variants in HSP90AA1 cause human male infertility? Summary answerVariants in HSP90AA1 appear as a possible autosomal dominant cause of human male infertility. What is known alreadyMale infertility is a highly heterogeneous condition, with so far over 300 genes described in this context. HSP90AA1 appears as a promising candidate gene for human male infertility, because the gene is highly conserved between species and knock-out of Hsp90aa1 in mice results in male-specific infert...

Prenatal alcohol exposure (PAE) disrupts embryonic development and gives rise to a variable fetal alcohol spectrum disorder (FASD) phenotype characterized by neurodevelopmental and dysmorphological defects. We investigated the effects of PAE on placental gene regulation by performing genome-wide DNA methylation (DNAm) microarray and gene expression (mRNA sequencing) analyses in 87 PAE, 77 unexposed control, and 11 smoking-exposed-only placentas. Significant alterations were identified in genes i...

Polygenic scores (PGSs) are widely used to summarize the joint genetic effects for disease-related traits. However, while age-dependent genetic effects are increasingly recognized, their integration into PGSs remains underexplored. Kidney function, assessed by estimated glomerular filtration rate (eGFR), has strong age-related genetic effects, and prediction of kidney function decline is an unmet need. We develop an age-informative PGS for quantitative traits by generating age-specific weights ...

Much remains unknown about the genetics of immune system changes during pregnancy. We used SNP data in a pregnancy cohort to genetically investigate 47 immune biomarkers at two timepoints, along with change between timepoints (delta). We identified 19 biomarkers with significant SNP-based heritability and 34 with genome-wide significant signals, demonstrating genetic regulation. The same biomarkers measured in early- and mid-pregnancy shared about half of significant associations across timepoin...

Genome wide association studies (GWAS), combined with fine-mapping have identified 196 independent signals associated with breast cancer risk. Deciphering the functional basis of these associations can inform our understanding of the biology and aetiology of breast cancer. Decoding GWAS risk associations is challenging due to linkage disequilibrium between variants and because most variants map to non-coding regions, influencing breast cancer risk via cis-regulatory mechanisms that modulate the ...

Until now, most genetic risk for vascular dementia (VD) remains unknown. Here, we firstly performed the largest cross-ancestry genome-wide association study meta-analysis comprising 5,886 VD and 1,027,883 controls of European, East Asian, South Asian, African, and Admixed American ancestry. We identified 37 genome-wide significant loci including CLU and APOE tagged by common variants and 35 loci tagged by rare variants, and demonstrated enrichment of VD heritability in lung and genetic associati...

The genetic relationship between asthma and lung function may be dependent on age-at-onset (AAO) of asthma. We investigated whether the shared genetics between asthma AAO and lung function is dependent on AAO. Asthma cases from UK Biobank were subset according to their AAO and genetic correlation was used to obtain genetically homogeneous groups, i.e., [≤]20 (LT20), 20-40, and >40 (GT40) years. Association analysis and fine-mapping were performed to identify shared genetics between AAO groups...

BackgroundRecent studies suggest that copy number variants (CNVs) may contribute to the missing heritability of complex diseases such as Alzheimers disease (AD) and related dementias (ADRD). MethodsWe performed a CNV analysis using genotyping data (Axiom 815K Spanish biobank array) from the GR@ACE/DEGESCO dementia dataset (n=20,067) of the Spanish population. Applying PennCNV and extensive quality control, 8,275 controls and 7,818 dementia cases were selected for gene-level case/control associa...

Hereditary ataxias are complicated neurological disorders with enormous genetic heterogeneity as well as the diverse genetic mechanism. Among different genetic mechanism, tandem nucleotide repeat expansion (TNRex) are the most common cause for genetic ataxias followed by single nucleotide variations in over 200 genes. The detection and the diagnosis of tandem nucleotide repeats in clinics and laboratories has been at large common in comparison with SNVs owing to the large number of the mutations...

Copy number variants (CNV) contribute significantly to the pathogenic variation associated with developmental disorders. CNV detection is often not included in standard exome sequencing (ES) analysis. Complementary methods such as chromosomal microarray are typically offered in diagnostic laboratories to diagnose pathogenic CNV. In this study, we aimed to develop an optimal approach for incorporating CNV detection within our ES analysis process for the Deciphering Developmental Disorders in Afri...

We assessed the impact of plasma protein quantitative trait loci (pQTL) on therapeutic hypotheses backed by human genetic evidence. We show that pQTL-supported target-indication pairs were 4.7 times more likely to advance from Phase I to launch, compared to a 2.6-fold increase observed only with human genetic evidence. Moreover, pQTL-based enrichment was prominent in druggable protein families which had limited enrichment from human genetic evidence alone.

Body mass index (BMI), type 2 diabetes (T2D) and associated cardiometabolic features modify Alzheimers disease (AD) risk, yet shared mechanisms remain poorly understood. Using sex- and age-stratified genotyping data for BMI and T2D, we investigate how these traits converge on shared genetic pathways to AD risk. Employing multi-trait, machine learning and single-cell transcriptomics, we identify sex-specific cardiometabolic liability linked to higher BMI-associated risk in women and T2D-driven ri...

Type 2 diabetes (T2D) affects 11.1% of the global population, underscoring the need for biomarkers that inform treatment response and glycemic outcomes. We evaluated the association between the FTO variant rs9939609-A and glycemic control in a Mexican population. A total of 174 individuals living with T2D from Merida and Sisal, Yucatan, were included, of whom 85% were receiving oral hypoglycemic agents as main treatment. Glycemic control was defined cross-sectionally as good ([≤]130 mg/dL, n=...

BackgroundHFE p.C282Y (c.845G>A; rs1800562) is a common missense mutation in persons of European ancestry, but we found no comprehensive tabulation of p.C282Y allele frequencies in Iberia. MethodsWe performed computerized and manual searches to identify evaluable reports of p.C282Y alleles in population/control cohorts [≥]50 subjects in Iberia. We tabulated numbers of subjects, nominal geographic sites of cohort recruitment, cohort characteristics, corresponding latitudes and longitudes, and...

BackgroundExternalizing behavior refers to emotional and behavioral problems or disorders characterized by conducts directed outward at an individuals environment. Polygenic scores (PGSs) indexing the individual genetic susceptibility for this behavior still explain a small proportion of the phenotypic variance. To increase this phenotypic variance explained for externalizing behavior we used a multi-PGS approach combining PGSs for several risk factors, mental health conditions and related pheno...

Hypothalamic-pituitary-adrenal axis (HPA axis) dysregulation is a risk factor for poor mental and physical health. Animal studies indicate that DNA methylation may be one mechanism through which stress can influence the function of the HPA axis, however human studies have not identified consistent individual loci. Machine learning can be used to develop methylation profile scores (MPSs), but this method has not yet been applied to HPA axis function. Using a novel machine learning pipeline, we de...

Irreversible profound hearing loss in early childhood impairs severely the development of spoken language, behavior and cognition. Hearing loss caused by aminoglycoside antibiotics in neonates treated for sepsis in intensive care units is linked to variants in the MT-RNR1 gene. Identifying the population at risk in acute medical settings is substantially limited by genotyping restricted to m.1555A>G only with 20% failure rate of the currently approved point-of-care test. We report an innovative ...

Predicting the pathogenic impact of missense variants is essential for understanding and diagnosing genetic diseases. These approaches have undergone significant evolution, with the latest methodologies based on deep learning approaches. Nonetheless, only a limited number use the potential of Protein Language Models (PLMs), which have demonstrated strong performance across various protein-related tasks. A new predictor, called PATHOS, was developed; it combines embeddings from an optimal set of...

ObjectiveThe most common forms of migraine are complex disorders characterized by significant clinical diversity. The genetic basis of migraine has been the subject of many studies but remains largely unknown. We present the first pilot genome-wide association study (GWAS) integrating a polygenic risk score (PRS) in the Portuguese population, designed to identify migraine susceptibility risk loci through a case-control study, in order to unravel population-specific variants. MethodsGenotyping w...