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Prostate Cancer
Volume 2019, Article ID 4047680, 11 pages
https://doi.org/10.1155/2019/4047680
Research Article

Interactions between Germline and Somatic Mutated Genes in Aggressive Prostate Cancer

Department of Genetics, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar St., New Orleans, LA 70112, USA

Correspondence should be addressed to Chindo Hicks; ude.cshusl@3kcihc

Received 18 December 2018; Revised 29 January 2019; Accepted 15 February 2019; Published 17 March 2019

Academic Editor: Cristina Magi-Galluzzi

Copyright © 2019 Tarun Karthik Kumar Mamidi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. L. Siegel, K. D. Miller, and A. Jemal, “Cancer statistics, 2017,” CA: A Cancer Journal for Clinicians, vol. 67, no. 1, pp. 7–30, 2017. View at Publisher · View at Google Scholar
  2. American Cancer Society, Cancer Facts and Figures 2017 (Annual Report).
  3. M. S. Litwin and H. Tan, “The diagnosis and treatment of prostate cancer,” Journal of the American Medical Association, vol. 317, no. 24, pp. 2532–2542, 2017. View at Publisher · View at Google Scholar
  4. L. M. FitzGerald, E. M. Kwon, M. P. Conomos et al., “Genome-wide association study identifies a genetic variant associated with risk for more aggressive prostate cancer,” Cancer Epidemiology, Biomarkers & Prevention, vol. 20, no. 6, pp. 1196–1203, 2011. View at Publisher · View at Google Scholar · View at Scopus
  5. C. Hicks, L. Miele, T. Koganti, and S. Vijayakumar, “Comprehensive assessment and network analysis of the emerging genetic susceptibility landscape of prostate cancer,” Cancer Informatics, vol. 12, pp. 175–191, 2013. View at Google Scholar · View at Scopus
  6. M. Aly, F. Wiklund, J. Xu et al., “Polygenic risk score improves prostate cancer risk prediction: Results from the Stockholm-1 cohort study,” European Urology, vol. 60, no. 1, pp. 21–28, 2011. View at Publisher · View at Google Scholar · View at Scopus
  7. N. Shao, Y. Zhu, and D. Ye, “Role of polygenic hazard score in prostate-specific antigen (PSA) screening for prostate cancer,” Translational Cancer Research, vol. 7, no. S7, pp. S743–S744, 2018. View at Publisher · View at Google Scholar
  8. A. Abeshouse, J. Ahn, R. Kbani et al., “The molecular taxonomy of primary prostate cancer,” Cell, vol. 163, no. 4, pp. 1011–1025, 2015. View at Google Scholar
  9. J. N. Weinstein, E. A. Collisson, G. B. Mills et al., “The cancer genome atlas pan-cancer analysis project,” Nature Genetics, vol. 45, no. 10, pp. 1113–1120, 2013. View at Google Scholar
  10. The International Cancer Genome Consortium, “International network of cancer genome projects,” Nature, vol. 464, pp. 993–998, 2010. View at Google Scholar
  11. Y. Wang, C. Wang, J. Zhang et al., “Interaction analysis between germline susceptibility loci and somatic alterations in lung cancer,” International Journal of Cancer, vol. 143, no. 4, pp. 878–885, 2018. View at Publisher · View at Google Scholar · View at Scopus
  12. H. S. Feigelson, K. A. B. Goddard, C. Hollombe et al., “Approaches to integrating germline and tumor genomic data in cancer research,” Carcinogenesis, vol. 35, no. 10, pp. 2157–2163, 2014. View at Publisher · View at Google Scholar · View at Scopus
  13. D. Welter, J. MacArthur, J. Morales et al., “The NHGRI GWAS Catalog, a curated resource of SNP-trait associations,” Nucleic Acids Research, vol. 42, no. 1, pp. D1001–D1006, 2014. View at Publisher · View at Google Scholar · View at Scopus
  14. J. P. A. Ioannidis, P. Boffetta, J. Little et al., “Assessment of cumulative evidence on genetic associations: Interim guidelines,” International Journal of Epidemiology, vol. 37, no. 1, pp. 120–132, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. M. J. Khoury, L. Bertram, P. Boffetta et al., “Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation and human diseases,” American Journal of Epidemiology, vol. 170, no. 3, pp. 269–279, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. G. S. Sagoo, J. Little, and J. P. Higgins, “Systematic reviews of genetic association studies,” PLoS Medicine, vol. 6, no. 3, p. e28, 2009. View at Publisher · View at Google Scholar
  17. D. Moher, A. Liberati, J. Tetzlaff, and D. G. Altman, “Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement,” Journal of Clinical Epidemiology, vol. 151, pp. 264–269, 2009. View at Google Scholar · View at Scopus
  18. A. Liberati, D. G. Altman, J. Tetzlaff et al., “The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: explanation and elaboration,” PLoS Medicine, vol. 6, Article ID e1000100, 2009. View at Google Scholar
  19. dbSNP, http://www.ncbi.nlm.nih.gov/SNP/.
  20. Human Genome Nomenclature Committee (HGNC), http://www.genenames.org/.
  21. M. S. Cookson, G. Aus, A. L. Burnett et al., “Variation in the definition of biochemical recurrence in patients treated for localized prostate cancer: the American urological association prostate guidelines for localized prostate cancer update panel report and recommendations for a standard in the reporting of surgical outcomes,” The Journal of Urology, vol. 177, no. 2, pp. 540–545, 2007. View at Publisher · View at Google Scholar · View at Scopus
  22. National Cancer Institute, Genomic Data Commons, https://gdc.cancer.gov/.
  23. M. E. Ritchie, B. Phipson, D. Wu et al., “Limma powers differential expression analyses for RNA-sequencing and microarray studies,” Nucleic Acids Research, vol. 43, no. 7, p. e47, 2015. View at Publisher · View at Google Scholar
  24. Y. Benjamini and Y. Hochberg, “Controlling the false discovery rate: a practical and powerful approach to multiple testing,” Journal of the Royal Statistical Society B: Methodological, vol. 57, no. 1, pp. 289–300, 1995. View at Google Scholar · View at MathSciNet
  25. Morpheus, https://software.broadinstitute.org/morpheus/.
  26. Ingenuity Pathways Analysis (IPA) System, Redwood, CA: Ingenuity Systems, http://www.ingenuity.com/.
  27. M. Ashburner, C. A. Ball, J. A. Blake et al., “Gene ontology: tool for the unification of biology,” Nature Genetics, vol. 25, no. 1, pp. 25–29, 2000. View at Publisher · View at Google Scholar · View at Scopus
  28. Y. Cheng, P. Yu, X. Duan et al., “Genome-wide analysis of androgen receptor binding sites in prostate cancer cells,” Experimental and Therapeutic Medicine, vol. 9, no. 6, pp. 2319–2324, 2015. View at Publisher · View at Google Scholar · View at Scopus
  29. H. H. Cheng, C. C. Pritchard, B. Montgomery, D. W. Lin, and P. S. Nelson, “Prostate cancer screening in a new era of genetics,” Clinical Genitourinary Cancer, vol. 15, no. 6, pp. 625–628, 2017. View at Publisher · View at Google Scholar · View at Scopus
  30. M. Gillard, J. Lack, A. Pontier et al., “Integrative genomic analysis of coincident cancer foci implicates CTNNB1 and PTEN alterations in ductal prostate cancer,” European Urology Focus, 2017. View at Publisher · View at Google Scholar
  31. S. Gupta, K. Iljin, H. Sara et al., “FZD4 as a mediator of ERG oncogene-induced WNT signaling and epithelial-to-mesenchymal transition in human prostate cancer cells,” Cancer Research, vol. 70, no. 17, pp. 6735–6745, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. P. Mariot, N. Prevarskaya, M. M. Roudbaraki et al., “Evidence of functional ryanodine receptor in apoptosis of prostate cancer (LNCaP) cells,” The Prostate, vol. 43, no. 3, pp. 205–214, 2000. View at Publisher · View at Google Scholar · View at Scopus
  33. H. Carter, R. Marty, M. Hofree et al., “Interaction landscape of inherited polymorphisms with somatic events in cancer,” Cancer Discovery, vol. 7, no. 4, pp. 410–423, 2017. View at Publisher · View at Google Scholar · View at Scopus
  34. N. Bonifaci, B. Górski, B. Masojć et al., “Exploring the Link between Germline and Somatic Genetic Alterations in Breast Carcinogenesis,” PLoS ONE, vol. 5, no. 11, p. e14078, 2010. View at Publisher · View at Google Scholar
  35. T. G. Grünewald and O. Delattre, “Cooperation between somatic mutations and germline susceptibility variants in tumorigenesis – a dangerous liaison,” Molecular & Cellular Oncology, vol. 3, no. 3, p. e1086853, 2015. View at Publisher · View at Google Scholar
  36. M. J. Machiela, B. M. Ho, V. A. Fisher, X. Hua, and S. J. Chanock, “Limited evidence that cancer susceptibility regions are preferential targets for somatic mutation,” Genome Biology, vol. 16, no. 1, article no. 193, 2015. View at Publisher · View at Google Scholar · View at Scopus
  37. K. L. Penney, J. A. Sinnott, S. Tyekucheva et al., “Association of prostate cancer risk variants with gene expression in normal and tumor tissue,” Cancer Epidemiology Biomarkers & Prevention, vol. 24, no. 1, pp. 255–260, 2015. View at Publisher · View at Google Scholar
  38. N. Larson, S. McDonnell, A. French et al., “Comprehensively evaluating cis -regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression,” American Journal of Human Genetics, vol. 96, no. 6, pp. 869–882, 2015. View at Publisher · View at Google Scholar
  39. C. Song, “Darwinian selection in prostate cancer and medical treatment,” International Journal of Clinical Medicine, vol. 08, no. 06, pp. 353–367, 2017. View at Publisher · View at Google Scholar
  40. D. V. Conti, K. Wang, X. Sheng, and J. T. Bensen, “Two novel susceptibility loci for prostate cancer in men of african ancestry,” Journal of the National Cancer Institute, vol. 9, no. 8, 2017. View at Google Scholar