e.g., SAMC013103; SAMN23469633; human
Accession SAMC389298
Sample name GP0581
Title GP0581
Sample type Clinical or host-associated pathogen
Organism Human gammaherpesvirus 4
Description A Comprehensive Risk Score for Effective Risk Stratification and Screening of Nasopharyngeal Carcinoma
Attributes
Isolate
Strain
Collected by China
Collection date 2014-05-07
Geographic location China: Guangxi
Host Homo sapiens
Host disease Nasopharyngeal carcinoma
Isolation source Saliva
Latitude and longitude 22.84 N 108.33 E
Culture collection
genotype
Host age
Host description
Host disease stage
Host health state
Host sex not applicable
Host subject id
Host tissue sampled
Passage history
Pathotype
Serotype
Serovar
Specimen voucher
Subgroup
Subtype
Release date 2021-06-03
BioProject Accession PRJCA005360
Submitter Miao  Xu  (xumiao@sysucc.org.cn)
Organization Sun Yat-sen University Cancer Center
Submission date 2021-06-06

Sample Data

Resource name Description
GVM (4)-
GVM000181Using Epstein-Barr virus (EBV)-based markers to screen populations at high risk for nasopharyngeal carcinoma (NPC) is an attractive preventive approach. Here, we developed a comprehensive risk score (CRS) that combined risk effects of EBV and human genetics for NPC risk stratification and validated this CRS within an independent, population-based dataset. Comparing the top decile with the bottom quintile of CRSs, the odds ratio of developing NPC is 21 (95% confidence interval: 12 - 37) in the validation dataset. When combining the top quintile of CRS with EBV serology tests currently used for NPC screening in southern China, the positive prediction value of screening increases from 4.70% (serology test alone) to 43.24% (CRS plus serology test). By identifying individuals at a monogenic level of NPC risk, this CRS approach provides new opportunities for personalized risk prediction and population screening in endemic areas for the early diagnosis and secondary prevention of NPC.
GVM000196Using Epstein-Barr virus (EBV)-based markers to screen populations at high risk for nasopharyngeal carcinoma (NPC) is an attractive preventive approach. Here, we develop a comprehensive risk score (CRS) that combines risk effects of EBV and human genetics for NPC risk stratification and validate this CRS within an independent, population-based dataset. Comparing the top decile with the bottom quintile of CRSs, the odds ratio of developing NPC is 21 (95% confidence interval: 12 - 37) in the validation dataset. When combining the top quintile of CRS with EBV serology tests currently used for NPC screening in southern China, the positive prediction value of screening increases from 4.70% (serology test alone) to 43.24% (CRS plus serology test). By identifying individuals at a monogenic level of NPC risk, this CRS approach provides opportunities for personalized risk prediction and population screening in endemic areas for the early diagnosis and secondary prevention of NPC.
GVM000647Abstract Epstein-Barr virus (EBV) and human leukocyte antigen (HLA) polymorphisms have shown the most prominent associations with the risk of nasopharyngeal carcinoma (NPC), a cancer that is endemic in southern China. Despite a priori biological knowledge that HLA genes are essential for the host immune response against viruses, the interplay between HLA genetics and EBV in the etiology of NPC is largely unknown. Using a population-based case-control study in NPC-endemic southern China, we apply a causal inference framework to disentangle interaction and mediation effects between two host HLA SNPs rs2860580 and rs2894207 and EBV variant 163364. We discover the strong interaction effects between the high-risk EBV subtype and both host SNPs on NPC risk within the original dataset and replicate the discovery of the significant interaction effects in an independent dataset (for rs2860580, relative excess risk due to interaction with EBV (RERI) = 4.08, 95% confidence interval (CI) = 2.03-6.14; for rs2894207, RERI = 3.37, 95% CI = 1.59-5.15). Interaction with the high-risk EBV accounts for the majority of the genetic effects of both host HLA SNPs on NPC risk. The effects of rs2860580 and rs2894207 on NPC risk mediated through increasing the frequency of the high-risk EBV are weak. These results indicate that host HLA genes and the high-risk EBV have a joint effect on NPC risk. Our study highlights that prevention strategies targeting the high-risk EBV subtype may largely reduce NPC risk associated with both EBV and host genetic susceptibility.
GVM000648Epstein-Barr virus (EBV) and human leukocyte antigen (HLA) polymorphisms have shown the most prominent associations with the risk of nasopharyngeal carcinoma (NPC), a cancer that is endemic in southern China. Despite a priori biological knowledge that HLA genes are essential for the host immune response against viruses, the interplay between HLA genetics and EBV in the etiology of NPC is largely unknown. Using a population-based case-control study in NPC-endemic southern China, we apply a causal inference framework to disentangle interaction and mediation effects between two host HLA SNPs rs2860580 and rs2894207 and EBV variant 163364. We discover the strong interaction effects between the high-risk EBV subtype and both host SNPs on NPC risk within the original dataset and replicate the discovery of the significant interaction effects in an independent dataset (for rs2860580, relative excess risk due to interaction with EBV (RERI) = 4.08, 95% confidence interval (CI) = 2.03-6.14; for rs2894207, RERI = 3.37, 95% CI = 1.59-5.15). Interaction with the high-risk EBV accounts for the majority of the genetic effects of both host HLA SNPs on NPC risk. The effects of rs2860580 and rs2894207 on NPC risk mediated through increasing the frequency of the high-risk EBV are weak. These results indicate that host HLA genes and the high-risk EBV have a joint effect on NPC risk. Our study highlights that prevention strategies targeting the high-risk EBV subtype may largely reduce NPC risk associated with both EBV and host genetic susceptibility.
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