NPJ Genomic Medicine最新文献

Despite advances in genome sequencing, many individuals with rare genetic disorders remain undiagnosed. Transcriptional profiling via RNA-seq can reveal functional impacts of DNA variants and improve diagnosis. We assessed blood-derived RNA-seq in the largely undiagnosed SickKids Genome Clinic cohort (n = 134), which has been subjected to multiple analyses benchmarking the utility of genome sequencing. Our RNA-centric analysis identifies gene expression outliers, aberrant splicing, and allele-specific expression. In one-third of diagnosed individuals (20/61), RNA-seq reinforced DNA-based findings. In 2/61 cases, RNA-seq revised diagnoses (EPG5 to LZTR1 in an individual with a Noonan syndrome-like disorder) and discovered an additional relevant gene (CEP120 in addition to SON in an individual with ZTTK syndrome). Additionally, ~7% (5/73) of undiagnosed cases had at least one plausible candidate gene identified. This study highlights both the benefits and limitations of whole-blood RNA profiling in refining genetic diagnoses and uncovering novel disease mechanisms.

The Genomic Medicine for Everyone (Geno4ME) study was established across the seven-state Providence Health system to enable genomics research and genome-guided care across patients' lifetimes. We included multi-lingual outreach to underrepresented groups, a novel electronic informed consent and education platform, and whole genome sequencing with clinical return of results and electronic health record integration for 78 hereditary disease genes and four pharmacogenes. Whole genome sequences were banked for research and variant reanalysis. The program provided genetic counseling, pharmacist support, and guideline-based clinical recommendations for patients and their providers. Over 30,800 potential participants were initially contacted, with 2716 consenting and 2017 having results returned (47.5% racial and ethnic minority individuals). Overall, 432 (21.4%) had test results with one or more management recommendations related to hereditary disease(s) and/or pharmacogenomics. We propose Geno4ME as a framework to integrate population health genomics into routine healthcare.

Saliva is an accessible biofluid with potential for non-invasive disease diagnostics. This study explores how genetic susceptibility to common diseases is reflected in DNA methylation (DNAm) and gene expression profiles in saliva. We constructed cis-mQTL (n = 345) and cis-eQTL (n = 277) datasets and examined correlations between DNAm and gene expression. Saliva QTLs were integrated with summary statistics from 36 genome-wide association studies (GWAS) using Summary-based Mendelian Randomization (SMR) to identify disease-associated molecular traits. We found 501 CpG sites and 24 genes as candidate biomarkers, as well as 56 eQTMs linked to conditions such as prostate cancer, squamous cell carcinoma, coronary artery disease, type 2 diabetes, and Parkinson's disease. This work introduces a publicly available resource and suggests that saliva-based molecular signatures may capture systemic disease risk, supporting future exploration as diagnostic markers.

Genome-wide association studies (GWAS) have established key role of immune dysfunction in Age-related Macular Degeneration (AMD), though the precise role of immune cells remains unclear. Here, we develop an explainable machine-learning pipeline (ML) using transcriptome data of 453 donor retinas, identifying 81 genes distinguishing AMD from controls (AUC-ROC of 0.80, CI 0.70-0.92). Most of these genes were enriched in their expression within retinal glial cells, particularly microglia and astrocytes. Their role in AMD was further strengthened by cellular deconvolution, which identified distinct differences in microglia and astrocytes between normal and AMD. We corroborated these findings using independent single-cell data, where several ML genes exhibited differential expression. Finally, the integration of AMD-GWAS data identified a regulatory variant, rs4133124 at PLCG2, as a novel AMD association. Collectively, our study provides molecular insights into the recurring theme of immune dysfunction in AMD and highlights the significance of glial cell differences in AMD progression.

Identifying critically ill newborns who will benefit from whole genome sequencing (WGS) is difficult and time-consuming due to complex eligibility criteria and evolving clinical features. The Mendelian Phenotype Search Engine (MPSE) automates the prioritization of neonatal intensive care unit (NICU) patients for WGS. Using clinical data from 2885 NICU patients, we evaluated the utility of different machine learning (ML) classifiers, clinical natural language processing (CNLP) tools, and types of Electronic Health Record (EHR) data to identify sick newborns with genetic diseases. Our results show that MPSE can identify children most likely to benefit from WGS within the first 48 h after NICU admission, a critical window for maximally impactful care. Moreover, MPSE provided stable, robust means to identify these children using many combinations of classifiers, CNLP tools, and input data types-meaning MPSE can be used by diverse health systems despite differences in EHR contents and IT support.

Pathogenic germline variants in telomerase (TERT) cause telomere biology disorders (TBDs) and are associated with bone marrow failure, pulmonary fibrosis, and other complications. TERT c.3150 G > C (p.K1050N) is frequent in the Ashkenazi Jewish (ASH) population and has been identified in ASH families with TBDs. Whole-genome sequencing of 96 p.K1050N heterozygotes from the UK Biobank and All of Us databases revealed a shared haplotype block, supporting a founder effect. Analyses of 15 additional p.K1050N cases validated this haplotype and identified mitochondrial and Y-STR haplogroups consistent with ASH ancestry. Clinical assessments showed that p.K1050N contributes to TBD phenotypes and shortened telomeres, while population data suggest incomplete penetrance. p.K1050N reduces telomerase activity and processivity, and decreases PCNA expression and BrdU incorporation, impairing cell proliferation. Our findings establish TERT p.K1050N as an ASH founder variant associated with TBDs, underscoring the need for genetic screening and long-term clinical studies.

RNA sequencing (RNA-seq) has become key to complementing exome and genome sequencing for variant interpretation. We present a minimally invasive RNA-seq protocol using short-term cultured peripheral blood mononuclear cells (PBMCs) with and without cycloheximide treatment, enabling detection of transcripts subject to nonsense-mediated decay. While broadly applicable, this protocol is particularly suited for neurodevelopmental disorders, as up to 80% of the genes in our intellectual disability and epilepsy gene panel are expressed in PBMCs. Applied to 46 affected individuals and 15 parents, RNA-seq revealed splicing defects in six of nine individuals with splice variants, allowing reclassification of seven variants. Targeted cDNA analysis confirmed aberrant splicing in four individuals but missed intron retention in two. Global analyses (FRASER, OUTRIDER, and monoallelic expression) supported findings but did not yield new diagnoses. We propose a flowchart integrating RNA-seq into diagnostic workflows. Overall, our protocol is easily implementable, captures complex splicing events, and enhances variant classification.

To identify novel genetic loci for children refractive error, we performed a meta-analysis of two genome-wide association studies (GWASs) of spherical equivalent (SE) in 1,237 children from the population-based Hong Kong Children Eye Study (HKCES) and the Low Concentration Atropine for Myopia Progression (LAMP) study. Replication was conducted in 4,093 Chinese children and 1,814 Chinese adults. Four lead-SNPs (MIR4275 rs292034, TENM3 rs17074027, LOC101928911 rs6925312 and FAM135B rs4609227) showed genome-wide significant association (P ≤ 5.0 × 10^-8) with SE. TENM3 had been associated with myopia in adults before, whilst the other three loci, MIR4275, LOC101928911 and FAM135B, were novel. Significant interaction between genetic risk scores (GRS) and near work on SE was also detected (β_interaction = 0.14, P_interaction = 0.0003). This study identified novel genetic loci for children refractive error and suggested myopia intervention can be individualized based on the genetic risk of children.

Individuals with germline PTEN variants (PHTS) have increased risks of the seemingly disparate phenotypes of cancer and neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD). Etiology of the phenotypic variability remains elusive. Here, we hypothesized that decreased genomic diversity, manifested by increased homozygosity, may be one etiology. Comprehensive analyses of 376 PHTS patients of European ancestry revealed significant enrichment of homozygous common variants in genes involved in inflammatory processes in the PHTS-NDD group and in genes involved in differentiation and chromatin structure regulation in the PHTS-ASD group. Pathway analysis revealed pathways germane to NDD/ASD, including neuroinflammation and synaptogenesis. Collapsing analysis of the homozygous variants identified suggestive modifier NDD/ASD genes. In contrast, we found enrichment of homozygous ultra-rare variants in genes modulating cell death in the PHTS-cancer group. Finally, homozygosity burden as a predictor of ASD versus cancer outcomes in our validated prediction model for NDD/ASD performed favorably.

Menière's disease (MD) is an inner ear disorder characterised by episodes of vertigo, sensorineural hearing loss and tinnitus linked to autoinflammation and/or type 2 immune response. We hypothesise that rare variation in immune response genes could drive the autoinflammatory phenotype in MD. We retrieved differentially expressed genes (DEG) from single-cell RNAseq and epigenomic datasets to search for rare variants in the MD exome (N = 454) and genome (N = 511) sequencing datasets. The variant chr1:10374335 C > T in the KIF1B gene was found in three MD unrelated individuals and was predicted to be likely pathogenic. According to differential transcript usage, transcript ENST00000622724.3 was found in MD samples, but absent in controls. Furthermore, this variant may influence splicing through the generation of exonic enhancers and silencers, potentially changing transcription factor binding at the promoter. These findings support that this KIF1B gene rare variant is associated with the MD autoinflammatory phenotype and may up-regulate its expression in monocytes.