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Биобанк ФГБУ «НМИЦ онкологии» Минздрава России как ресурс для проведения исследований в области персонифицированной медицины
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Kit OI, Timofeeva SV, Sitkovskaya AO, Novikova IA, Kolesnikov EN. The biobank of the National Medical Research Centre for Oncology as a resource for research in the field of personalized medicine: A review. Journal of Modern Oncology. 2021;24(1):6–11. DOI: 10.26442/18151434.2022.1.201384
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Ключевые слова: биобанк, персонифицированная медицина, онкология, биомаркер
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Biobanks are the platform for innovative biomedical research in the field of translational and personalized medicine. The important aspect for conducting large-scale research in the field of genomics, transcriptomics, proteomics is the availability of a sample information of the documented high-resolution samples. The biobanks solve the problem of forming groups of patients with different nosology within the population of interest and provide clinical and laboratory information on each sample. The aim of this article is to describe the Biobank processes of the National Medical Research Centre for Oncology within the framework of existing projects and build up collections. The review discusses the main stages of the systematized biobank process, describes the methods of sample preparation of different types of biological material, and also provides statistics of the build up collections. To this date, the predominant part of the depository consists of tissue samples of patients diagnosed with colorectal cancer 24% and stomach cancer 23% of the total number of tissue samples, while the number of tissue samples of pancreatic cancer is 10%, and esophageal cancer and breast cancer – 22%. In addition to tissue samples, the biobank of the National Medical Research Centre for Oncology stores 24 cell lines of a human origin and the collection of 200 microbiota samples: 100 are from patients diagnosed with lung cancer and 100 from conditional healthy donors. Currently, the studies have been performed on biomaterial from the biobank build up collections to search for prognostic biomarkers and potential targets for targeted therapy by using high-throughput sequencing in patients diagnosed with pancreatic cancer and brain cancer. Thus, the collections play an important role for research in the field of personalized medicine, providing early diagnosis and effective treatment for each patient.
Keywords: biobank, personalized medicine, oncology, biomarker, Russia
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DOI:10.1038/bjc.2016.304
2. Swede H, Stone CL, Norwood AR. National population-based biobanks for genetic research. Genet Med. 2007;9(3):141-9. DOI:10.1097/gim.0b013e3180330039
3. Goetz LH, Schork NJ. Personalized medicine: motivation, challenges, and progress. Fertil Steril. 2018;109(6):952-63. DOI:10.1016/j.fertnstert.2018.05.006
4. Drapkina OM. Russian National Association of Biobanks and Biobanking Specialists – a tool for integrating Russian biobanks and increasing the efficiency of biomedical research. Cardiovascular Therapy and Prevention. 2020;19(6):2757 (in Russian). DOI:10.15829/1728-8800-2020-2757
5. Braun KL, Tsark JU, Powers A, et al. Cancer patient perceptions about biobanking and preferred timing of consent. Biopreserv Biobank. 2014;12(2):106-12. DOI:10.1089/bio.2013.0083
6. Patil S, Majumdar B, Awan KH, et al. Cancer oriented biobanks: A comprehensive review. Oncol Rev. 2018;12(1):357. DOI:10.4081/oncol.2018.357
7. Coppola L, Cianflone A, Grimaldi AM, et al. Biobanking in health care: evolution and future directions. J Transl Med. 2019;17(1):172. DOI:10.1186/s12967-019-1922-3
8. Liu A, Pollard K. Biobanking for Personalized Medicine. Adv Exp Med Biol. 2015;864:55-68. DOI:10.1007/978-3-319-20579-3_5
9. Samokhina IV, Sagakyants AB. Work within the COVID-19 pandemic – the experience of the biobank of the National Medical Research Center of Oncology. Cardiovascular Therapy and Prevention. 2020;19(6):2741 (in Russian). DOI:10.15829/1728-8800-2020-2741
10. Kotikalapudi R, Patel RK. Comparative study of the influence of EDTA and sodium heparin on long term storage of cattle DNA. Cell J. 2015;17(1):181-6.
DOI:10.22074/cellj.2015.526
11. Sidstedt M, Hedman J, Romsos EL, et al. Inhibition mechanisms of hemoglobin, immunoglobulin G, and whole blood in digital and real-time PCR. Anal Bioanal Chem. 2018;410(10):2569-83. DOI:10.1007/s00216-018-0931-z
12. UK Biobank, 2007. Protocol for A Large-Scale Prospective Epidemiological Resource. UK Biobank Coordinating Centre; Stockport, UK: Protocol No: UKBB‑PROT-09-06 (Main Phase).
13. Nagai A, Hirata M, Kamatani Y, et al. Overview of the BioBank Japan Project: Study design and profile. J Epidemiol. 2017;27(3S):S2-8. DOI:10.1016/j.je.2016.12.005
14. Victorian Cancer Biobank, 2020. Available at: https://viccancerbiobank.org.au/ Accessed: 30.10.2021.
15. Canadian Tissue Repository Network, 2020. Available at: https://www.ctrnet.ca/ Accessed: 30.10.2021.
16. Terveer EM, van Beurden YH, Goorhuis A, et al. How to: Establish and run a stool bank. Clin Microbiol Infect. 2017;23(12):924-30. DOI:10.1016/j.cmi.2017.05.015
17. Pel J, Leung A, Choi WWY, et al. Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers. PLoS One. 2018;13(12):e0208283. DOI:10.1371/journal.pone.0208283
18. Woo PC, Lau SK, Teng JL, et al. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect. 2008;14(10):908-34. DOI:10.1111/j.1469-0691.2008.02070.x
19. Thomas T, Gilbert J, Meyer F. Metagenomics – a guide from sampling to data analysis. Microb Inform Exp. 2012;2(1):3. DOI:10.1186/2042-5783-2-3
20. Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.
DOI:10.1186/s12915-014-0087-z
21. Cuthbertson L, Rogers GB, Walker AW, et al. Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections. J Clin Microbiol. 2014;52(8):3011-6. DOI:10.1128/JCM.00764-14
22. Choo JM, Leong LE, Rogers GB. Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep. 2015;5:16350. DOI:10.1038/srep16350
23. Smirnova DV, Zalomova LV, Zagainova AV, et al. Cryopreservation of the human gut microbiota: Current state and perspectives. Int J Med Microbiol. 2019;309(5):259‑69. DOI:10.1016/j.ijmm.2019.06.001
24. Межевова И.В., Ситковская А.О., Кит О.И. Первичные культуры опухолевых клеток: современные методы получения и поддержания in vitro. Южно-российский онкологический журнал. 2020;1(3):36-49 [Mezhevova IV, Sitkovskaya AO, Kit OI. Primary tumor cell cultures: сurrent methods of obtaining and subcultivation. South Russian Journal of Cancer. 2020;1(3):36-49 (in Russian)]. DOI:10.37748/2687-0533-2020-1-3-4
25. Shamova TV, Sitkovskaya AO, Rostorguev EE, et al. Preparation of primary glial tumor cell lines. Permskii meditsinskii zhurnal. 2020;37(5):79-89 (in Russian). DOI:10.17816/pmj37579%89
26. Kit OI, Gvaldin DY, Trifanov VS, et al. Molecular-genetic features of pancreatic neuroendocrine tumors. Russian Journal of Genetics. 2020;56(1):142-60 (in Russian). DOI:10.31857/S001667582002006X
27. Pushkin AA, Timoshkina NN, Rostorguev EЕ, et al. Expression status of 15th genes in glial tumors of the brain. Sovremennye problemy nauki i obrazovaniya. 2019;5:230 (in Russian).
ФГБУ «Национальный медицинский исследовательский центр онкологии» Минздрава России, Ростов-на-Дону, Россия
*timofeeva.sophia@gmail.com
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Oleg I. Kit, Sofia V. Timofeeva*, Anastasiya O. Sitkovskaya, Inna A. Novikova, Evgeniy N. Kolesnikov
National Medical Research Centre for Oncology, Rostov-on-Don, Russia
*timofeeva.sophia@gmail.com