NPJ Genomic Medicine最新文献

Neurodevelopmental disorders (NDDs) have a strong but largely unexplained genetic basis. Moreover, the genetic architecture of these complex disorders in under-represented communities is poorly studied. We analyzed 110 probands from 100 families (for a total of 298 individuals), using whole genome sequencing (WGS) to identify genetic contributors to NDDs. This study is part of the '5000genomi@VdA' project characterizing Valle d'Aosta (Italy) genomic landscape in health and disease. Probands were stratified into three diagnostic categories: ASD (autism spectrum disorder without intellectual disability), ID (intellectual disability without ASD), and ASD-ID (autism spectrum disorder with comorbid intellectual disability). Following the ACMG guidelines, we identified 32 likely phenotype-causing variants in known NDD-associated genes in 26.4% of the probands. We observed a diagnostic yield gradient, lowest in ASD, intermediate in ASD-ID, and highest in ID. We also identified 42 variants of uncertain significance, 14 of which were located in genes not previously linked to NDDs but relevant to neurodevelopment, and may thus represent new NDD candidate genes. Furthermore, we used Evo 2, an evolutionary constraint-based model, to refine variant interpretation and identify VUS with pathogenic-like signatures. These findings highlight the utility of WGS in exploring the genetic heterogeneity within stratified NDD clinical groups.

Age-related macular degeneration (AMD) is the leading cause of vision loss in the aged population with the late stage geographic atrophy (GA). Risk factors for AMD include age, genetic variants in the complement system, nutritional factors, and alterations in the gut microbiome (GM). To identify taxonomic and functional differences in the microbiome associated to disease pathophysiology and genetic risk factors, this study investigated the GM and the ocular surface microbiome (OSM) of GA patients compared to healthy controls by whole-metagenome shotgun sequencing. 16 AMD-associated SNPs were genotyped from blood samples using TaqMan assays and Sanger sequencing. While GA patients showed differences in the GM, and altered metabolic pathways including inosine 5'-phosphate degradation, NAD salvage, and ketogenesis, no alterations in the OSM were found. Genetic analysis associated SNP rs1061170 in the complement factor H gene with GA. These findings suggest that microbial alterations may contribute to GA through inflammation and oxidative stress.Registry: ClinicalTrials.gov, NCT02438111, Registration date: 28 April 2015, and NCT04658238, Registration date: 01 December 2020.

Moyamoya disease (MMD) is a progressive cerebrovascular disorder with intracranial arterial stenosis and collateralization. Over 70% of sporadic cases lack known genetic drivers; RNF213 variants explain only 23% of Chinese cases, highlighting unmet diagnostic and therapeutic needs. Trio-based whole-exome sequencing (WES) of 126 Chinese sporadic MMD patients (30 pediatric-parent trios) underwent cross-platform validation, cohort screening (n = 268), and functional analysis in human brain microvascular endothelial cells (HBMECs). Variants were prioritized by population frequency, pathogenicity, and case-control comparisons. Endothelial function and oxidative stress were assessed via proliferation, migration, tube formation, and molecular markers. WES identified 42 rare sporadic and 15 de novo mutations; Sanger validation confirmed 11 sporadic/11 de novo variants including de novo NF1 p.Q2002X and recurrent CARS1 p.E712V. CARS1 p.E712V carriers showed early-onset stenosis (mean age 7.5 ± 4.4 years) and right-dominant Suzuki stage ≥4, while NF1 p.Q2002X correlated with severe bilateral stenosis in a child (onset age 3). CARS1 p.E712V showed significant patient enrichment (P = 0.004). Silencing NF1/CARS1 in HBMECs enhanced proliferation, migration, tube formation, and reduced GPX4 (CARS1-specific). CARS1 mutation augmented angiogenesis, indicating functional alteration. This study identifies NF1 and CARS1 as novel susceptibility genes for sporadic MMD in Chinese, expanding the genetic landscape beyond RNF213.

CYP2C19 and CYP2D6 are involved in the hepatic metabolism of approximately 35-40% of clinically used drugs. We conducted an in vivo phenotyping study encompassing 114 Estonian Biobank participants to evaluate the functional impact of rare or novel single-nucleotide and structural variants in the CYP2C19 and CYP2D6 genes using omeprazole and metoprolol as respective probe drugs. Plasma concentrations of these drugs and their metabolites were measured at 10 time points, and parent drug-to-metabolite ratios were calculated to determine enzymatic activity. Long-read sequencing enabled high-resolution star allele calling. Our results provide the first in vivo confirmation that partial gene and intragenic deletions in CYP2C19 (CYP2C19*37 and CYP2C19*42), enriched in Estonians and Finns, are associated with poor metaboliser phenotypes (P < 1.2 × 10^-7). Additionally, we offer in vivo evidence of reduced metabolic activity of the CYP2D6*124 allele and a novel missense variant (c.940C>A) in exon 6 of CYP2D6. Furthermore, we observed that inhibitor exposure was significantly associated with higher metabolic ratios for both CYP2C19 (P = 3.0 × 10^-6) and CYP2D6 (P = 0.02). Our findings emphasise the importance of identifying genetic variants in CYP2C19 and CYP2D6 beyond commonly assessed star alleles and that profiling for drug interactions can provide more precise assignments of metabolic phenotypes and improve personalised treatment.

Fabry disease (FD) is a rare X-linked lysosomal storage disorder caused by variants in the alpha-galactosidase A gene (GLA). Cardiac complications are a major cause of mortality, but the large number of variants complicate early identification of at-risk patients. In this study, we assessed the microcirculation using Retinal Vessel Analysis (RVA) in 63 FD patients age- and gender-matched to 60 healthy controls, analyzing associations between RVA parameters, cardiac involvement, and GLA variants. FD patients showed reduced venular flicker-induced dilation, narrower retinal arterioles, and a lower arteriolar-to-venular ratio. Impaired retinal microcirculation was associated with cardiac involvement, and patients with cardiac-associated GLA variants exhibited narrower retinal arterioles. Markers of inflammation and endothelial dysfunction (ED) were significantly higher in FD patients. Higher inflammatory levels correlated with altered retinal microcirculation in patients carrying cardiac-associated GLA variants. RVA detects microvascular ED in FD patients and may serve as a non-invasive biomarker for cardiovascular risk stratification. Registration: https://clinicaltrials.gov/study/NCT06758648 ; Unique identifier: NCT06758648.

Structural variants (SVs) that disrupt topologically associating domains can cause disease by rewiring enhancer-promoter interactions. Duplications involving GPR101 are known to cause X-linked acrogigantism (X-LAG) through ectopic GPR101 expression, but not all of these duplications are pathogenic. This presents a diagnostic challenge, especially in the prenatal setting. We evaluated POSTRE, a tool that predicts the regulatory impact of SVs, to distinguish pathogenic from benign GPR101 duplications. We analyzed seven non-pathogenic duplications and 27 known X-LAG-associated duplications. To enable predictions in an X-LAG-relevant tissue, enhancer maps built using H3K27ac ChIP-seq, ATAC-seq, and RNA-seq data derived from human anterior pituitary samples (NIH research protocol 97-CH-0076, Clinicaltrials.gov Identifier NCT00001595, submitted on 11 March 1999) were integrated into POSTRE. POSTRE correctly classified all 34 duplications as benign or pathogenic. In addition, one X-LAG case with mild clinical features (i.e. severe growth hormone hypersecretion without pituitary tumorigenesis) was found to include only 2/5 VGLL1 enhancers, whereas all typical X-LAG cases had ≥4 enhancers duplicated. This suggests that partial enhancer hijacking at VGLL1 could explain the different clinical features in this individual. These findings support the utility of POSTRE to support diagnostic pipelines when interpreting SVs affecting chromatin architecture in pituitary disease and highlight its potential to reduce uncertainty in genetic counseling without requiring chromatin conformation capture assays.

Recently, some clinics have begun using preimplantation genetic testing for monogenic disorders (PGT-M) for moderately penetrant breast cancer (BC) risk variants, while other clinics use polygenic risk scores (PRS) in the context of preimplantation embryo screening. Using both simulation and formal mathematical approaches, we evaluated: (1) in what circumstances embryo selection using PRS could lead to systematically erroneous results due to failure to consider monogenic carrier status; and (2) whether PGT-M for moderate penetrance variants could lead to erroneous results due to unassessed, yet elevated PRS. Variants in BRCA1, BRCA2, and PALB2 resulted in a risk distribution that was essentially disjoint from the non-carriers, regardless of PRS. By contrast, for moderately penetrant genes, standard PGT-M would fail to select the lowest risk embryo approximately 5% of the time due to elevated PRS. This complex interplay suggests that caution should be exercised when considering preimplantation genetic testing involving exclusively monogenic variants of moderate penetrance or polygenic scores.

Reproductive carrier screening has evolved beyond ethnic-specific testing to include diverse populations, yet gene selection varies considerably. In Singapore, genomic data analysis identified severe paediatric conditions amongst Chinese, Indian and Malay populations absent from existing screening panels. We developed a model leveraging data from 9051 participants to guide gene selection for carrier screening representative of Asian genetic diversity, focusing on severe paediatric-onset conditions prevalent in these populations. After evaluating severity, genotype-phenotype variability, clinical utility and technical feasibility, we identified 88 genes associated with recessive severe paediatric onset prevalent amongst Chinese, Indian and Malay populations, irrespective of carrier frequency. Including 24 additional genes from our registry resulted in a 105-gene panel, predicted to identify 0.44% at-risk couples, with 86 genes overlapping existing panels. Broadening criteria to include moderate severity conditions while limiting carrier frequencies to less than 1 in 200 reduced the panel to 59 genes, increasing predicted at-risk couples to 0.47%, due to higher carrier frequencies, yet introducing counselling complexities from greater clinical variability. Using local genomic data, we identified genetic conditions relevant to Asian populations for carrier screening. Expanding national genomic sequencing initiatives provides an opportunity to assess genetic condition prevalence across diverse ancestries, improving equity in carrier screening programmes.

We present a rare case of low-grade diffusely infiltrative tumor (LGDIT), SMARCB1-mutant, recurred as an atypical teratoid/rhabdoid tumor (AT/RT) seven years after complete resection. Comprehensive genetic and epigenetic analysis of both LGDIT, SMARCB1-mutant, and AT/RT samples revealed that SMARCB1 mutation and methylation patterns are stable during the latent period and not the direct target that determines the malignant phenotype of cancer. However, there was a switch of oncogenic signaling pathways from the MAPK pathway to the PI3K/AKT pathway with accumulation of somatic variants responsible for the inherent malignant phenotype. Considering the dormant oncogenic traits behind an innocent phenotype, it is recommended to confirm the diagnosis of LGDIT, SMARCB1-mutant, by conducting a methylation classifier analysis or an SMARCB1 expression study to ensure accurate prognosis prediction.