GoKawiilStudy participants
Participants from southern China were enrolled through two independent recruitments (sample sets 1 and 2). Participants in sample set 1 were participants in a population-based case–control study conducted in NPC-endemic regions of southern China (Guangdong and Guangxi provinces) between 2010 and 2014. The study design was previously described in detail59. In brief, 2,554 treatment-naive patients histologically confirmed with NPC were identified through a rapid case ascertainment system involving a network of local physicians. For the population-based control recruitment, 2,648 healthy control individuals were frequency-matched to cases by sex, 5-year age group and residential area, and were randomly selected from local population registries. Saliva DNA samples were available for 1,202 cases and 1,780 controls. In sample set 1, 747 patients with NPC and 1,251 healthy controls with age, sex, and available EBV genotype and host genome-wide genotyping were included in the discovery phase of the host genome-wide scan (Extended Data Fig. 1, Supplementary Table 1 and Supplementary Fig. 2). In sample set 2, an independent NPC case–control study was recruited from the same Chinese population in southern China. This study consisted of 883 cases and 1,537 controls of self-reported Chinese ancestry recruited between 2013 and 2022. For sample set 2, 644 patients with NPC and 880 healthy participants with age, sex, and available EBV genotype and host genome-wide genotyping were included in the validation phase of host genome-wide interaction study (Extended Data Fig. 1, Supplementary Table 1 and Supplementary Fig. 2). All study participants were recruited irrespective of EBV strain status, and no selection was performed on the basis of infection with any specific EBV subtypes.
The Singapore dataset was completely independently recruited in Singapore, comprising 226 cases with NPC and 209 controls. Among these, 223 cases with NPC and 204 healthy controls with available EBV genotype and HLA allele data were included in the replication of EBV subtype–host interaction analysis (Extended Data Fig. 1 and Supplementary Fig. 4).
Furthermore, to capture EBV genomic diversity across China for viral population genetic and phylogenetic analysis, we enrolled 163 healthy participants from different regions of China, including northern China (Shandong, Shanxi, Inner Mongolia, Xinjiang, Hebei and Liaoning), eastern China (Fujian) and southwestern China (Sichuan). Among them, 113 EBV whole-genome sequences passed quality control (see details below) and were included in subsequent EBV phylogenetic analyses (Extended Data Fig. 1, Supplementary Table 16 and Supplementary Fig. 7).
This study was approved by the institutional ethics committees of the Sun Yat-sen University Cancer Center, Guangzhou, China and the Genome Institute of Singapore, A*STAR, Singapore. Written informed consent was obtained from all participants.
Sample collection and processing
Saliva samples were collected into vials containing an equal volume of prepared lysis buffer (50 mM Tris, pH 8.0, 50 mM EDTA, 50 mM sucrose, 100 mM NaCl and 1% SDS) and stored at −80 °C. DNA was extracted from saliva using either the Chemagic STAR (Hamilton Robotics) or the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer’s instructions. The extracted DNA was subsequently used for human and EBV genotyping, as well as EBV whole-genome sequencing.
Peripheral blood samples were collected and processed within 24 h. Human peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll density gradient centrifugation, cryopreserved in liquid nitrogen and subsequently used for T cell functional assays.
Data acquisition and processing
The majority of the paired data used for the host–EBV interaction analyses were newly generated in this study (Extended Data Fig. 1). For host genome genotyping, all data used in the genome-wide interaction scan (n = 3,522) were generated for this study, comprising case–control datasets for the host genome-wide interaction analysis with high-risk EBV status (step 1: 747 cases and 1,251 controls in discovery; and 644 cases and 880 controls in validation). For EBV whole-genome sequences, this study in total included 732 newly sequenced EBV genomes, together with 1,354 EBV genomes from NCBI databases. The EBV genome-wide interaction fine-mapping was conducted in the paired host–EBV genome dataset (n = 734), within which 154 out of 734 EBV genomes were previously deposited in the NCBI in our earlier work6,44.
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