Human Genomics最新文献

Background: Inherited retinal degeneration (IRD) comprises a diverse group of monogenic disorders characterized by marked genetic and phenotypic heterogeneity. Although next-generation sequencing (NGS) enables the identification of candidate variants, many remain classified as variants of uncertain significance (VUS). Ancestry-matched population data can strengthen comparative evidence, and the emergence of national biobanks provides new opportunities to operationalize ACMG/AMP criterion PS4 through case-control analyses.

Methods: We integrated an IRD cohort of 802 probands with whole-genome allele frequency data from 1,492 individuals in the Taiwan Biobank. An allele-based case-control framework was applied, assigning PS4 when the Haldane-Anscombe-corrected odds ratio was ≥ 5 and the 95% confidence interval excluded 1. Post-PS4 triage required variants to: (i) reside in IRD-associated genes, (ii) be rare in East Asian populations in gnomAD v4.1, and (iii) be annotated in RefSeq as exonic, untranslated regions, or splicing (± 20 bp). Baseline ACMG/AMP classifications were generated using GeneBe and finalized through expert curation.

Results: Incorporation of PS4 substantially refined variant interpretation, upgrading two variants from Likely Pathogenic to Pathogenic and six from VUS to Likely Pathogenic. Homozygous exemplar variants, including CNGB1 (NM_001297.5): c.2921T > G and CFAP410 (NM_004928.3): c.340_351dup, demonstrated strong genotype-phenotype concordance with confirmatory sequencing, illustrating an end-to-end workflow from statistical enrichment to clinical reporting.

Conclusion: An ancestry-aware case-control framework enables effective implementation of PS4 and improves the accuracy of IRD variant classification. This reproducible strategy supports the integration of population-specific genomic data into clinical workflows and is applicable to other monogenic disorders.

Background: Colorectal cancer (CRC) is the third most common cancer globally. Alternative splicing contributes significantly to CRC tumorigenesis through aberrant transcript generation. However, the regulatory influence of RNA modifications on splicing remains poorly understood, largely due to technical difficulty. Nanopore direct RNA sequencing addresses this by enabling simultaneous detection of RNA modifications and Alternative splicing events (ASEs).

Methods: We conducted Nanopore direct RNA sequencing on paired tumor and normal tissues from surgical resections at Beijing Hospital. Differential putative RNA modification sites and ASEs linked to CRC were systematically identified. To validate the key findings, we utilized a large patient cohort from The Cancer Genome Atlas (TCGA) and predicted 3D protein structures with AlphaFold3. The predicted structures were then compared using TM-align. Regulatory relationships between RNA modifications and splicing were explored through predictive modeling of potential cis-regulatory pairs. The splicing events were also validated.

Results: The MYH11-201 transcript of the MYH11 gene contains an additional exon (ENSE00001632812) compared to the MYH11-203 isoform. Both bioinformatic analysis and experimental validation confirmed frequent loss of this exon in tumor tissues. This finding was further validated in the TCGA cohort, demonstrating a significant preference for exon skipping in tumor tissues. These results suggest that the skipping of ENSE00001632812 is a promising candidate biomarker associated with CRC pathogenesis. Notably, this exon's PF00063 domain interacts with multiple tumor suppressor genes and oncogenes domains, suggesting its functional importance. The structures revealed pronounced rotational divergence within a putative C-terminal transmembrane domain-like region. Furthermore, we utilized Nanopore sequencing to explore the potential interplay between alternative splicing and RNA modifications. We implemented an integrated analytical workflow (available at https://github.com/lelelililele/Nanopore-ASEs-and-RNA-modification ) combining modification calling and splicing analysis tools to investigate RNA modification-related enzymes and splicing-related proteins in CRC.

Conclusions: This pilot study utilizes Nanopore direct RNA sequencing to characterize exon skipping events and RNA modifications in CRC. We identified the skipping of MYH11 exon ENSE00001632812 as a potential candidate for future diagnostic investigation. By integrating modification and splicing data, we highlighted putative regulatory pairs that warrant further functional exploration. While our findings offer new insights into CRC molecular mechanisms, extensive validation in independent large-scale cohorts and functional assays is essential to confirm the diagnostic utility and mechanistic roles of these targets.

Background: Wilson disease is a rare autosomal recessive disorder caused by variations in ATP7B, leading to copper accumulation and multisystemic damage. Diagnosis is often delayed due to its heterogeneous clinical presentation and limited genetic data in underrepresented populations.

Methods: We characterized ten Ecuadorian patients with clinical suspicion of Wilson disease using whole-exome sequencing (WES), selected to enable simultaneous assessment of ATP7B and other metabolic genes relevant to Wilson-like phenotypes. Variants were interpreted following HGNC and ACMG/AMP guidelines. Ancestry was examined in nine patients using ADMIXTURE and PCA with a reference panel of 968 individuals from African, European, and Indigenous American populations. ATP7B expression was quantified by RT-qPCR in the one patient lacking identifiable coding-region variants.

Results: Six patients were homozygous and two were compound heterozygous for pathogenic or likely pathogenic ATP7B variants. The recurrent alleles c.2052dupC p.(Met685*) (Guayaquil) and c.2012_2013insAT p.(Met671Ilefs*) (Cañar/Cuenca) showed geographic and ancestry patterns consistent with known demographic structure in Ecuador, though not sufficient to infer founder effects. Additional variants included c.3188 C > T p.(Ala1603Val), c.3727 C > G p.(Leu1243Val), c.2318G > A p.(Cys773Tyr), and c.2080 C > T p.(Arg694Trp). One patient with no detectable ATP7B coding-region variation demonstrated ~ 9.8-fold reduced ATP7B expression, supporting the clinical diagnosis.

Conclusions: This study provides an integrated clinical, molecular, and ancestry framework for characterizing Wilson disease in an underrepresented population. The identification of regionally recurrent ATP7B variants, together with the diversity of clinical presentations, highlights the need for comprehensive diagnostic approaches in admixed populations. Larger studies incorporating segregation and functional assays will be essential to refine variant interpretation and improve access to molecular diagnosis in Latin America.