An Integrative Analysis of Nasopharyngeal Carcinoma Genomes Unraveled Unique Processes Driving a Viral-Positive Cancer
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Integration
2.2. Whole-Exome Sequencing (WES) Data Analysis
2.3. Identification of Driver Genes and Timing of Somatic Mutations
2.4. Signature Analysis
2.5. Clonal Deconvolution
2.6. Integrate Survival Analysis
3. Results
3.1. Compiling the Largest Cohort of NPC Genomes
3.2. Integrative Analysis Uncovered Many Novel Driver Genes for NPC
3.3. “Missing Driver Events” in NPC
3.4. Larger Sample Size Empowers Copy Number Identification
3.5. Novel Mutational Signatures across the NPC Cohort
3.6. An Integrative Survival Model for NPC
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Group | Percentage (Value) |
---|---|
Observations | |
363 | |
Stage | |
I | 2.8% (10) |
II | 8.5% (31) |
III | 33% (121) |
IV | 19% (69) |
missing | 36% (132) |
Age | |
Mean (SD) | 50 (12) |
valid (missing) | 232 (131) |
Gender | |
Female | 15% (54) |
Male | 49% (178) |
missing | 36% (131) |
Smoking | |
No | 28% (103) |
Yes | 29% (105) |
missing | 43% (155) |
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Liu, X.; Li, Y.; Zhou, X.; Zhu, S.; Kaya, N.A.; Chan, Y.S.; Ma, L.; Xu, M.; Zhai, W. An Integrative Analysis of Nasopharyngeal Carcinoma Genomes Unraveled Unique Processes Driving a Viral-Positive Cancer. Cancers 2023, 15, 1243. https://doi.org/10.3390/cancers15041243
Liu X, Li Y, Zhou X, Zhu S, Kaya NA, Chan YS, Ma L, Xu M, Zhai W. An Integrative Analysis of Nasopharyngeal Carcinoma Genomes Unraveled Unique Processes Driving a Viral-Positive Cancer. Cancers. 2023; 15(4):1243. https://doi.org/10.3390/cancers15041243
Chicago/Turabian StyleLiu, Xiaodong, Yanjin Li, Xiang Zhou, Sinan Zhu, Neslihan A. Kaya, Yun Shen Chan, Liang Ma, Miao Xu, and Weiwei Zhai. 2023. "An Integrative Analysis of Nasopharyngeal Carcinoma Genomes Unraveled Unique Processes Driving a Viral-Positive Cancer" Cancers 15, no. 4: 1243. https://doi.org/10.3390/cancers15041243
APA StyleLiu, X., Li, Y., Zhou, X., Zhu, S., Kaya, N. A., Chan, Y. S., Ma, L., Xu, M., & Zhai, W. (2023). An Integrative Analysis of Nasopharyngeal Carcinoma Genomes Unraveled Unique Processes Driving a Viral-Positive Cancer. Cancers, 15(4), 1243. https://doi.org/10.3390/cancers15041243