Rapid advancement in cancer genomic big data in the pursuit of precision oncology
DOI:
https://doi.org/10.13181/mji.rev.204250Keywords:
cancer genetic database, oncology, personalized medicineAbstract
In the current big data era, massive genomic cancer data are available for open access from anywhere in the world. They are obtained from popular platforms, such as The Cancer Genome Atlas, which provides genetic information from clinical samples, and Cancer Cell Line Encyclopedia, which offers genomic data of cancer cell lines. For convenient analysis, user-friendly tools, such as the Tumor Immune Estimation Resource (TIMER), which can be used to analyze tumor-infiltrating immune cells comprehensively, are also emerging. In clinical practice, clinical sequencing has been recommended for patients with cancer in many countries. Despite its many challenges, it enables the application of precision medicine, especially in medical oncology. In this review, several efforts devoted to accomplishing precision oncology and applying big data for use in Indonesia are discussed. Utilizing open access genomic data in writing research articles is also described.
Downloads
References
The Economist. The world's most valuable resource is no longer oil, but data [Internet]. The Economist; 2017 [cited 2018 Aug 25]. Available from: https://www.economist.com/leaders/2017/05/06/the-worlds-most-valuable-resource-is-no-longer-oil-but-data.
Hinkson IV, Davidsen TM, Klemm JD, Chandramouliswaran I, Kerlavage AR, Kibbe WA. A comprehensive infrastructure for big data in cancer research : accelerating cancer research and precision medicine. Front Cell Dev Biol. 2017;5:108. https://doi.org/10.3389/fcell.2017.00083
Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, et al. Big data : astronomical or genomical ? PLoS Biol. 2015;13(7):e1002195. https://doi.org/10.1371/journal.pbio.1002195
Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45(10):1113-20. https://doi.org/10.1038/ng.2764
Tomczak K, Czerwi?ska P, Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol. 2015;19(1A):A68-77. https://doi.org/10.5114/wo.2014.47136
National Cancer Institute. The Cancer Genome Atlas: Program Overview [Internet]. 2016 [cited 2018 Aug 20]. Available from: https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga.
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, et al. Comprehensive characterization of cancer driver genes and mutations. Cell. 2018;173(2):371-85.e18. https://doi.org/10.1016/j.cell.2018.02.060
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, et al. Oncogenic signaling pathways in The Cancer Genome Atlas. Cell. 2018;173(2):321-37.e10. https://doi.org/10.1016/j.cell.2018.03.035
Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, et al. An Integrated TCGA Pan-Cancer clinical data resource to drive high-quality survival outcome analytics. Cell. 2018;173(2):400-16.e11. https://doi.org/10.1016/j.cell.2018.02.052
Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483(7391):603-7. https://doi.org/10.1038/nature11003
Permata TB, Hagiwara Y, Sato H, Yasuhara T, Oike T, Gondhowiardjo S, et al. Base excision repair regulates PD-L1 expression in cancer cells. Oncogene. 2019;38:4452-66. https://doi.org/10.1038/s41388-019-0733-6
Sato H, Niimi A, Yasuhara T, Permata TB, Hagiwara Y, Isono M, et al. DNA double-strand break repair pathway regulates PD-L1 expression in cancer cells. Nat Commun. 2017;8:1751. https://doi.org/10.1038/s41467-017-01883-9
Pan D, Kobayashi A, Jiang P, de Andrade LF, Tay RE, Luoma AM, et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science. 2018;359(6377):770-5. https://doi.org/10.1126/science.aao1710
Shen J, Ju Z, Zhao W, Wang L, Peng Y, Ge Z, et al. ARID1A deficiency promotes mutability and potentiates therapeutic antitumor immunity unleashed by immune checkpoint blockade. Nat Med. 2018;24(5):556-62. https://doi.org/10.1038/s41591-018-0012-z
Nuryadi E, Sasaki Y, Hagiwara Y, Permata TB, Sato H, Komatsu S, et al. Mutational analysis of uterine cervical cancer that survived multiple rounds of radiotherapy. Oncotarget. 2018;9(66):32642-52. https://doi.org/10.18632/oncotarget.25982
Cortes-Ciriano I, Lee S, Park WY, Kim TM, Park PJ. A molecular portrait of microsatellite instability across multiple cancers. Nat Commun. 2017;8:15180. https://doi.org/10.1038/ncomms15180
Lee HJ, Palm J, Grimes SM, Ji HP. The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations. Genome Med. 2015;7:112. https://doi.org/10.1186/s13073-015-0226-3
Chin L, Andersen JN, Futreal PA. Cancer genomics: from discovery science to personalized medicine. Nat Med. 2011;17(3):297-303. https://doi.org/10.1038/nm.2323
Dancey JE, Bedard PL, Onetto N, Hudson TJ. The genetic basis for cancer treatment decisions. Cell. 2012;148(3):409-20. https://doi.org/10.1016/j.cell.2012.01.014
Li T, Fan J, Wang B, Traugh N, Chen Q, Liu JS, et al. TIMER: a web server for comprehensive analysis of tumor-infiltrating immune cells. Cancer Res. 2017;77(21):e108-10. https://doi.org/10.1158/0008-5472.CAN-17-0307
Li B, Severson E, Pignon JC, Zhao H, Li T, Novak J, et al. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol. 2016;17(1):174. https://doi.org/10.1186/s13059-016-1028-7
Zhang J, Bajari R, Andri D, Gerthoffert F, Lepsa A, Nahal-Bose H, et al. The International Cancer Genome Consortium data portal. Nat Biotech. 2019;37:367-9. https://doi.org/10.1038/s41587-019-0055-9
Permata TB, Utami IG, Gondhowiardjo S. Towards precison oncology and the need for Asian cancer genomic big data. In: FARO 3rd Annual Meeting: Cancer free world, making it a reality. Shenzhen: Federations of Asian Radiation Oncology (FARO); 2019.
Nuryadi E, Permata TB, Komatsu S, Oike T, Nakano T. Inter-assay precision of clonogenic assays for radiosensitivity in cancer cell line A549. Oncotarget. 2018;9(17):13706-12. https://doi.org/10.18632/oncotarget.24448
Hodson R. Precision medicine. Nature. 2016;537:S49. https://doi.org/10.1038/537S49a
Kohno T. Implementation of "clinical sequencing" in cancer genome medicine in Japan. Cancer Sci. 2018;109(3):507-12. https://doi.org/10.1111/cas.13486
Saito M, Momma T, Kono K. Targeted therapy according to next generation sequencing - based panel sequencing. Fukushima J Med Sci. 2018;64(1)9-14. https://doi.org/10.5387/fms.2018-02
Published
How to Cite
Issue
Section
License
Authors who publish with Medical Journal of Indonesia agree to the following terms:
- Authors retain copyright and grant Medical Journal of Indonesia right of first publication with the work simultaneously licensed under a Creative Commons Attribution-NonCommercial License that allows others to remix, adapt, build upon the work non-commercially with an acknowledgment of the work’s authorship and initial publication in Medical Journal of Indonesia.
- Authors are permitted to copy and redistribute the journal's published version of the work non-commercially (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in Medical Journal of Indonesia.
