dbGVOSCC: a comprehensive database of genetic variation for systems genetics research on oral squamous cell carcinoma

TL;DR

dbGVOSCC is a new database that compiles genetic variations related to oral squamous cell carcinoma, supporting research into its genetic causes and potential treatments.

Contribution

dbGVOSCC provides a comprehensive, curated database of genetic variations in oral squamous cell carcinoma with integrated bioinformatics tools.

Findings

The database includes 1,788 genetic variation entries from 400 studies and 106,079 clinical samples.

PPI analysis identified 15 key genes like TP53 and EGFR involved in OSCC pathways.

User testing showed high usability scores (SUS 88.75 and NPS 90).

Abstract

Oral squamous cell carcinoma (OSCC) is a highly aggressive malignancy of the oral epithelium, marked by a high rate of lymph node metastasis and a profound negative impact on patients’ quality of life. Despite its severity, no routine screening program currently exists for OSCC. To address the genetic heterogeneity underlying OSCC, we have developed a database of genetic variation in oral squamous cell carcinoma (dbGVOSCC; http://www.sysbio.org.cn/dbGVOSCC/).

OSCC literature (1991–2024) was queried from PubMed and screened manually and via PubTator, following predefined inclusion/exclusion criteria. Entities and relations were extracted from qualifying articles and organized into tables. The database adopted a browser/server architecture using HTML and XAMPP. Front-end was built with HTML and CSS for web display; server-side used Apache for infrastructure, MySQL for data management, and PHP/JavaScript for backend-frontend integration. Bioinformatics included mapping genes to STRING (confidence >0.9), hub gene identification via PPI degree centrality, and GO/KEGG enrichment with clusterProfiler (FDR-corrected). Usability was assessed using SUS and NPS surveys.

dbGVOSCC comprises 1,788 somatic genetic variation entries from 400 original studies and 106,079 clinical samples, covering epimutations/methylations (329), SNPs (411), point mutations excluding SNP (258), indels (98), CNVs (348), LOH (28), one locus mutation, plus 333 unspecified mutations. We curated 817 biomarker-linked variations (diagnostic n=71, therapeutic n=175, prognostic n=291; 277 multi-application). PPI analysis highlighted 15 key genes (e.g., TP53, CTNNB1, AKT1, EGFR, PIK3CA). Enrichment implicated proliferation, adhesion/migration, p53/DNA damage response, and PI3K–Akt signaling. User testing showed SUS 88.75 (grade A) and NPS 90.

dbGVOSCC represents a robust and reliable knowledge base, offering clinicians and researchers an open-source platform for personalized genotype-phenotype association studies and systems genetics research into the mechanisms of OSCC.

Figures