Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) exhibits unusual geographic restriction despite ubiquitous lifelong infection. Screening programs can detect most NPC cases at an early stage, but existing EBV diagnostics are limited by false positives and low positive predictive value (PPV), leading to excess screening endoscopies, MRIs, and repeated testing. Recent EBV genome-wide association studies (GWAS) suggest that EBV BALF2 variants account for more than 80% of attributable NPC risk. We therefore hypothesized that high-risk BALF2 variants could be readily detected in plasma for once-lifetime screening triage. We designed and validated a multiplex genotyping assay to detect EBV BALF2 polymorphisms in human plasma. Targeted next-generation sequencing was used to validate this assay, conduct association studies with clinical phenotype, and longitudinally genotype plasma to assess within-host haplotype stability. We examined the association between NPC and BALF2 haplotypes in a large non-endemic population and three prior EBV GWAS. Finally, we estimated NPC mortality reduction, resource utilization, and cost-effectiveness of BALF2 variant-informed screening using a previously-validated cohort model. Following analytical validation, the BALF2 genotyping assay had 99.3% concordance with sequencing in a cohort of 24 NPC cases and 155 non-NPC controls. BALF2 haplotype was highly associated with NPC in this non-endemic population (I613V: odds ratio [OR] 7.9; V317M: OR 178.8). No other candidate BALF2 polymorphisms were significantly associated with NPC or hematologic disorders. Longitudinal genotyping revealed 97.8% within-host haplotype concordance, indicative of lifelong latent infection. In a meta-analysis of 755 NPC cases and 981 non-NPC controls, BALF2 I613V and V317M were significantly associated with NPC in both endemic and non-endemic populations. Modeled variant-informed screening strategies achieved a 46% relative increase in PPV with 7% decrease in effective screening sensitivity, thereby averting nearly half of screening endoscopies/MRIs among endemic populations in east/southeast Asia. EBV BALF2 haplotypes are temporally stable within hosts and can be readily detected in plasma via an inexpensive multiplex genotyping assay that offers near-perfect sequencing concordance. In endemic and non-endemic populations, I613V and V317M were highly associated with NPC and could be leveraged to develop variant-informed screening programs that mitigate false positives with small reductions in screening sensitivity.

中文翻译：

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多重 Epstein-Barr 病毒 BALF2​​ 基因分型可检测血浆中的高风险变异，用于鼻咽癌人群筛查

爱泼斯坦-巴尔病毒 (EBV) 相关鼻咽癌 (NPC) 尽管终生感染无处不在，但仍表现出不寻常的地域限制。筛查程序可以在早期发现大多数 NPC 病例，但现有的 EBV 诊断受到假阳性和低阳性预测值 (PPV) 的限制，导致过度筛查内窥镜、MRI 和重复检测。最近的 EBV 全基因组关联研究 (GWAS) 表明 EBV BALF2​​ 变体占可归因 NPC 风险的 80% 以上。因此，我们假设高风险 BALF2​​ 变体可以很容易地在血浆中检测到，用于终生筛查分类。我们设计并验证了一种用于检测人血浆中 EBV BALF2​​ 多态性的多重基因分型分析。靶向二代测序用于验证该测定，进行与临床表型和纵向基因型血浆的关联研究，以评估宿主内单倍型的稳定性。我们检查了大型非流行人群和三个先前的 EBV GWAS 中 NPC 和 BALF2​​ 单倍型之间的关联。最后，我们使用先前验证的队列模型估计了 BALF2​​ 变异知情筛查的 NPC 死亡率降低、资源利用和成本效益。在分析验证后，BALF2​​ 基因分型测定与 24 名 NPC 病例和 155 名非 NPC 对照的队列中的测序有 99.3% 的一致性。在这个非流行人群中，BALF2​​ 单倍型与 NPC 高度相关（I613V：优势比 [OR] 7.9；V317M：OR 178.8）。没有其他候选 BALF2​​ 多态性与 NPC 或血液疾病显着相关。纵向基因分型显示 97。8% 的宿主内单倍型一致性，表明终生潜伏感染。在对 755 例 NPC 病例和 981 例非 NPC 对照的荟萃分析中，BALF2​​ I613V 和 V317M 在地方性和非地方性人群中均与 NPC 显着相关。模型化的变异知情筛查策略使 PPV 相对增加了 46%，有效筛查敏感性降低了 7%，从而避免了东亚/东南亚流行人群中近一半的筛查内窥镜/MRI。EBV BALF2​​ 单倍型在宿主体内是暂时稳定的，并且可以通过提供近乎完美的测序一致性的廉价多重基因分型测定法在血浆中轻松检测到。在流行和非流行人群中，