ABSTRACT
Liver cancer, a main cause of death, is extremely difficult to be diagnosed at its early stages. On a positive side, predicting the disease development or progression by analyzing medical data can be helpful for the future early diagnosis and accordingly the increase of the patients' survival. Medical investigation and researchers raise that Single nucleotide polymorphisms in certain apoptosis-related genes are related to the cancer development. The objective of this paper is to find quantitative associations between apoptotic gene-related polymorphisms and the progression level of the liver cancer. To find these associations, Association rule mining is applied using the Frequent Pattern algorithm. An experimental study on an Egyptian cohort of 1246 patients with advanced cirrhosis and liver cancer resulted in associations which can serve as novel biomarkers. It has been found that CDKN2A and HLA-DP genes have relation to the HCC development with a confidence value 0.55, and CDKN1B and Il28b, are related to the liver cancer progression with a confidence value 0.54.
- Gary L. Davis et al. 2008. Hepatocellular carcinoma: management of an increasingly common problem. Baylor University Medical Center Proceedings, 21(3), 266--280.Google ScholarCross Ref
- T. Gameel, S. Rady, K. El-Bahnasy and S. Kamal.2017. Prediction of liver cancer development risk in genotype 4 Hepatitis C patients using knowledge discovery modeling. In Eighth International Conference on Intelligent Computing and Information Systems (ICICIS),(Cairo, Egypt), 410--415.Google Scholar
- Amal S. Ibrahim, Hussein M. Khaled, Nabiel NH Mikhail, Hoda Baraka, and Hossam Kamel. 2014. Cancer Incidence in Egypt: Results of the National Population-Based Cancer Registry Program. Journal of Cancer Epidemiology.Google ScholarCross Ref
- Nobuhiro Tsuchiya, Yu Sawada, Itaru Endo, Keigo Saito, Yasushi Uemura, and Tetsuya Nakatsura.2015. Biomarkers for the early diagnosis of hepatocellular carcinoma. World J Gastroenterol, 21(37), 10573--10583.Google ScholarCross Ref
- X. Ding and X. Guo.2018.A survey of SNP Data Analysis. Big Data Mining and Analytics, 1(3), 173--190.Google ScholarCross Ref
- Yanxun Xu, Xiaofeng Zheng, Yuan Yuan, Marcos R. Estecio, Jean-Pierre Issa, Peng Qiu, Yuan Ji, and Shoudan Liang.2014. BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data. IEEE/ACM Transactions on computational biology and bioinformatics, 11, 1038--1044. Google ScholarDigital Library
- F Jin, WJ Xiong, JC Jing, Z Feng, LS Qu and XZ Shen.2011.Evaluation of the association studies of single nucleotide polymorphisms and hepatocellular carcinoma: a systematic review. J Cancer Res Clin Oncol., 137, 1095--1104.Google ScholarCross Ref
- N Nishida and M Kudo.2013.Recent advancements in comprehensive genetic analyses for human hepatocellular carcinoma.Oncology, 4, 93--97.Google Scholar
- TC Chen, KF Ng, JM Lien, LB Jeng, MF Chen and LL Hsieh.2000 Mutational analysis of the p27(kip1) gene in hepatocellular carcinoma.Cancer Lett., 153, 169--173.Google Scholar
- F Liu, YG Wei, LM Luo, WT Wang, LN Yan, TF Wen, MQ Xu, JY Yang and B Li. 2013. Genetic variants of p21 and p27 and hepatocellular cancer risk in a Chinese Han population: a case-control study. Int J Cancer, 132, 2056--2064.Google ScholarCross Ref
- Y Xu, et al.2011.Potentially functional polymorphism in the promoter region of miR-34b/c is associated with an increased risk for primary hepatocellular carcinoma. Int J Cancer, 128,412--417.Google ScholarCross Ref
- B. Deng et al, 2013. Association of a p73 exon 2 G4C14-to-A4T14 polymorphism with risk of hepatocellular carcinoma in a Chinese population.Tumour Biol., 34293--299.Google Scholar
- M. Fumagalli, et al. 2012. Telomeric DNA damage is irreparable and causes persistent DNA-damage-response activation.Nature Cell Biology, 14(5), 555.Google Scholar
- EH Blackburn. 2001. Switching and signaling at the telomere. Cell., 106(6), 661--673.Google ScholarCross Ref
- J. Jiang, et al. 2015. Structure of Tetrahymena telomerase reveals previously unknown subunits, functions, and interactions. SCIENCE, 350.Google Scholar
- J. Shay. 2016. Role of Telomeres and Telomerase in Aging and Cancer. Cancer Discov, 6(6), 584--593.Google ScholarCross Ref
- F. Pinheiro, M. Kuo, A. Thomo and J. Barnett. 2013. Extracting association rules from liver cancer data using the fp-growth algorithm, In IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).Google Scholar
- X. ZHAI, Q. XUE, Q. LIU, Y. GUO and Z. CHEN.2017. Classifier of cross talk genes predicts the prognosis of hepatocellular carcinoma. Molecular Medicine Reports, 16, 3253--3261.Google ScholarCross Ref
- J. Ma, et al. 2017. BMP4 enhances hepatocellular carcinoma proliferation by promoting cell cycle progression via ID2/CDKN1B signaling. Molecular Carcinogenesis, 56, 2279--2289.Google ScholarCross Ref
- F. Fornari, et al. 2008. MiR-221 controls CDKN1C/p57 and CDKN1B/p27 expression in human hepatocellular carcinoma. Oncogene, 27, 5651--5661.Google ScholarCross Ref
- M. El-Awady, et al. 2012. Association of IL28B SNP with progression of Egyptian HCV Genotype 4 patients to end stage liver disease.Hepat Mon.., 12, 271--277.Google Scholar
- K. Schulze, et al.2015.Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic target,. Nature Genetics, 47, 505--511.Google ScholarCross Ref
- X. Zhang, et al. 2015.Relationship between HLA-DP gene polymorphisms and the risk of hepatocellular carcinoma: a meta-analysis. Genetics and Molecular Research, 14, 15553--15563.Google ScholarCross Ref
- L. Yu, et al. 2015. Quantitative assessment of common genetic variations in HLA-DP with hepatitis B virus infection, clearance and hepatocellular carcinoma development. Nature, Scientific Reports.Google Scholar
- T. le and D. Lo. 2015. Beyond support and confidence: Exploring interestingness measures for rule-based specification mining.In IEEE 22nd International Conference on software analysis, Evolution and Reengineering (SANER).Google Scholar
- Snezhana Sulova. 2018. Association Rule Mining for Improvement of IT Project Management. TEM Journal, 7(4), 717--722.Google Scholar
- Hanirex DK, Thooyamani KP and Khanaa V.2017.Performance of association rules for Dengue Virus Type1 amino acids using an Integration of Transaction Reduction and Random Sampling (TRRS) algorithm. Int J Pharm Sci Res., 8(6), 2578--87.Google Scholar
Index Terms
- Novel Biomarkers from genes in the apoptotic pathway for Prediction of HCC Progression using Association Rule Mining
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