研究成果

Background: High-throughput sequencing has revolutionized genetic disorder diagnosis, but variant pathogenicity interpretation is still challenging. Even though the human genome variation society (HGVS) provides recommendations for variant nomenclature, discrepancies in annotation remain a significant hurdle. Results: In this study, we evaluated the annotation concordance between three tools-ANNOVAR, SnpEff, and variant effect predictor (VEP)-using 164,549 two-star variants from ClinVar. The analysis used HGVS nomenclature string-match comparisons to assess annotation consistency from each tool, corresponding coding impacts, and associated ACMG criteria inferred from the annotations. The analysis revealed variable concordance rates, with 58.52% agreement for HGVSc, 84.04% for HGVSp, and...

Evaluating robustness of somatic mutation detections is essential when using whole-exome sequencing (WES) for treatment decision-making. A comprehensive evaluation was conducted using tumor WES from the US Food and Drug Administration-led Sequencing Quality Control Phase 2 project, in which multiple library kits sequenced identical DNA materials across three laboratories to benchmark analytical validity. These workflows included various read aligner (BWA, Bowtie2, DRAGEN-Aligner, DRAGMAP, and HISAT2) and mutation caller (Mutect2, TNscope, DRAGEN-Caller, and DeepVariant) combinations. The results revealed that DRAGEN exhibited superior performance, achieving mean F1 scores of 0.966 and 0.791 for single-nucleotide variant and insertion/deletion detection, respectively. Among open-source...

Background and objectives: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study. Methods: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine...

Animal growth is driven by the collective actions of cells, which are reciprocally influenced in real-time by the animal's overall growth state. Whereas cell behavior and animal growth state are expected to be tightly coupled, it is not yet determined whether local cellular features at the micrometer scale might correlate with the body size of an animal at the macroscopic level. By inputting 722 skin cell images and corresponding size data for each zebrafish larva into machine learning models, we determined that the Vision Transformer (ViT) with a random cropping and voting strategy was able to achieve high predictive performance (F-score of 0.91). Remarkably, analyzing as few as 27 skin cells within a single image of 0.01 mm2 was sufficient to predict the individual's overall...

Trichomes in Prunus persica (L.) Batsch are crucial specialized structures that play a protective role against both biotic and abiotic stresses. The fruits with and without trichomes are respectively named as peach and nectarine. At the genetic level, the formation of trichome in peach is controlled by a single gene, PpMYB25, at the G locus. Peach (GG or Gg) is dominant to nectarine (gg), but such regulatory role was reported in a small-scale accession. In this study, we performed large-scale genotype and phenotype screening on 295 accessions. Almost all accessions supported the casual relationship between trichome formation and PpMYB25. However, a peach to nectarine mutant, named Maravilha Nectarine Mutant (MN), was discovered to possess a putative functional PpMYB25 gene sequence (Gg)...

Background: Pathogenic variants in OTOF are a major cause of auditory synaptopathy. However, challenges remain in interpreting OTOF variants, including difficulties in confirming haplotype phasing using traditional short-read sequencing (SRS) due to the large gene size, the potential incomplete penetrance of certain variants, and difficulties in assessing variants at non-canonical splice sites. This study aims to revisit the genetic landscape of OTOF variants in a Taiwanese non-syndromic auditory neuropathy spectrum disorder (ANSD) cohort using a combination of sequencing technologies, predictive tools, and experimental validations. Methods: We performed SRS to analyze OTOF variants in 65 unrelated Taiwanese patients diagnosed with non-syndromic ANSD, complemented by long-read sequencing...

Background: Atrial fibrillation (AF) is a major risk factor for transient ischemic attack (TIA)/ischemic stroke (IS). Objectives: Given the dynamic nature of IS risk, this study aimed to predict IS risk in AF patients using a high-dimensional time-series model. Methods: We conducted a cohort study at the National Taiwan University Hospital from 2014 to 2019, including 7,710 AF patients, with external validation in 6,822 patients from the National Taiwan University Hospital Yunlin Branch. The Forecasting Strokes via Interpretable Independent Networks (ForeSIIN) model, based on gated recurrent units, was proposed. Kaplan-Meier analysis with log-rank test evaluated risk group differences. Results: The annual TIA/IS incidence rate ranged from 181.96 (95% CI: 164.42-200.93) to 15.81 (95% CI:...

Breast cancer stands as one of the most prevalent malignancies affecting women. Alterations in molecular pathways in cancer cells represent key regulatory disruptions that drive malignancy, influencing cancer cell survival, proliferation, and potentially modulating therapeutic responsiveness. Therefore, decoding the intricate molecular mechanisms and identifying novel therapeutic targets through systematic computational approaches are essential steps toward advancing effective breast cancer treatments. In this study, we developed an integrative computational framework that combines single-cell RNA sequencing (scRNA-seq) and multi-omics analyses to delineate the functional characteristics of malignant cell subsets in breast cancer patients. Our analyses revealed a significant correlation...

Neuroblastoma is an aggressive childhood cancer that arises from the sympathetic nervous system. Despite advances in treatment, high-risk neuroblastoma remains difficult to manage due to its heterogeneous nature and frequent development of drug resistance. Drug repurposing guided by single-cell analysis presents a promising strategy for identifying new therapeutic options. Here, we aim to characterize high-risk neuroblastoma subpopulations and identify effective repurposed drugs for targeted treatment. We performed single-cell transcriptomic analysis of neuroblastoma samples, integrating bulk RNA-seq data deconvolution with clinical outcomes to define distinct malignant cell states. Using a systematic drug repurposing pipeline, we identified and validated potential therapeutic agents...

Betalains, a group of pigments widely distributed in various plants, are extensively applied in the food, beverage, and medicinal industries. The biosynthesis of betalains involves the enzymatic action of 4,5-DOPA-dioxygenase, which catalyzes the key ring-opening reaction of DOPA to produce betalamic acid, a crucial intermediate in the pathway. The crystal structure of a 4,5-DOPA-dioxygenase from Beta vulgaris (BvDOD) was determined in this study. The structural analysis revealed that BvDOD exhibited a structural fold similar to that of other members of the extradiol dioxygenase family. Moreover, the Fe-ligand residues His15, His53, and His229 indicated the enzyme's reliance on nonheme iron for catalyzing the ring-opening reaction. Molecular docking and mutational analysis identified...