2026 Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE) : Submission #1

Abstract Summary Testicular germ cell tumor (TGCT) is the most common cancer in young adult individuals and exhibits one of the highest heritability estimates among solid tumors. Familial aggregation studies consistently indicate a strong genetic component to TGCT susceptibility, with risk pathways enriched for cell‑cycle regulation, chromosome segregation, and DNA repair mechanisms. Although genome‑wide association studies (GWAS) and transcriptome‑wide association studies (TWAS) have identified numerous germline risk loci, the underlying biological mechanisms and causal variants remain poorly defined.
Methods: We implemented an integrative analytic framework to functionally annotate TGCT risk regions identified through GWAS and TWAS. For each region, we defined a set of credible variants using LD ≥0.8 with the lead SNP. These variants were evaluated using histone‑mark profiles, chromatin accessibility, regulatory element predictions, and long‑range chromatin interaction datasets (Hi‑C) to assess potential enhancer or promoter activity. This enhancer‑focused screen was applied uniformly across all loci; however, each region was additionally examined for alternative mechanisms, including post‑transcriptional regulation.
Results: The chromosome 7 locus illustrates how this approach resolves locus‑specific molecular mechanisms. TWAS and GWAS jointly prioritized SP4 as a candidate gene. Within the credible set, we identified rs7798894, located in the SP4 3′UTR, as the most plausible functional variant. rs7798894 alters a predicted binding site for hsa‑miR‑4282, a microRNA reported to exhibit tumor‑suppressive activity. The T allele (frequency ~0.72) creates a functional miRNA seed site, whereas the A allele (frequency ~0.28) disrupts it, suggesting allele‑specific SP4 regulation. Although enhancer annotations were surveyed, the miRNA‑mediated mechanism provided the strongest functional explanation for this locus.
Conclusions: Our integrative GWAS–TWAS framework enables locus‑specific mechanistic inference and highlights post‑transcriptional miRNA targeting as a driver of risk at the chromosome 7 SP4 locus. This approach improves causal variant identification, informs biologically grounded polygenic risk score development, and advances mechanistic understanding of TGCT susceptibility.