Статья
Развитие биомедицины сопровождается появлением новых технологий, методов диагностики и лечения, а также возможностей применения в медицинской практике новых типов биологических мишеней, в частности, нуклеиновых кислот. В качестве объектов генетических исследований используют геномную дезоксирибонуклеиновую кислоту (ДНК), внеклеточную ДНК (вкДНК) и ДНК микробиоты, получаемые из разных типов образцов: тканей, крови и ее производных, кала и др. Использование новых технологий для ДНК-анализа потребовало разработки стандартизованных методов процессинга биообразцов с целью получения качественных образцов ДНК. В научно-медицинских исследованиях применяются различные методы сбора, пробоподготовки и хранения разных видов ДНК-содержащего биоматериала, выделенной ДНК и методы оценки качества биообразцов, а также стандарты биобанкирования. Очевидно, что использование единых стандартов позволит проводить крупномасштабные генетические исследования на базе биобанков и отдельных научных лабораторий. Активное участие во внедрении единых стандартов биобанкирования принимают специалисты профессиональных организаций, таких как ISBER (International Society for Biological and Environmental Repositories), BBMRI-ERIC (Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium), ESBB (European, Middle Eastern & African Society for Biopreservationa and Biobanking) и российская Национальная ассоциация биобанков и специалистов по биобанкированию (НАСБИО).
1. Lappalainen T, Scott AJ, Brandt M, et al. Genomic Analysis in the Age of Human Genome Sequencing. Cell. 2019;177:70–84. doi:10.1016/j.cell.2019.02.032.
2. Schübeler D. Function and information content of DNA methylation. Nature. 2015;517:321–326. doi:10.1038/nature14192.
3. Siravegna G, Marsoni S, Siena S, et al. Integrating liquid biopsies into the management of cancer. Nat Rev Clin Oncol. 2017;14:531–548. doi:10.1038/nrclinonc.2017.14.
4. Hoffmann AR, Proctor LM, Surette MG, et al. The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals. Vet Pathol. 2016;53:10–21. doi:10.1177/0300985815595517.
5. Liang D, Leung RKK, Guan W, et al. Involvement of gut microbiome in human health and disease: Brief overview, knowledge gaps and research opportunities. Gut Pathog. 2018. p. 3. doi:10.1186/s13099-018-0230-4.
6. Anhê FF, Varin T V., Le Barz M, et al. Gut Microbiota Dysbiosis in Obesity-Linked Metabolic Diseases and Prebiotic Potential of Polyphenol-Rich Extracts. Curr Obes Rep. 2015;4:389–400. doi:10.1007/s13679-015-0172-9.
7. Carding S, Verbeke K, Vipond DT, et al. Dysbiosis of the gut microbiota in disease. Microb Ecol Heal Dis. 2015;26. doi:10.3402/mehd.v26.26191.
8. Chen J, Domingue JC, Sears CL. Microbiota dysbiosis in select human cancers: Evidence of association and causality. Semin Immunol. 2017;32:25–34. doi:10.1016/j.smim.2017.08.001.
9. Drapkina OM, Kaburova AN. Gut microbiota composition and metabolites as the new determinants of cardiovascular pathology development. Ration Pharmacother Cardiol. 2020;16:277–285. (In Russ.) doi:10.20996/1819-6446-2020-04-02.
10. Shendure J, Balasubramanian S, Church GM, et al. DNA sequencing at 40: Past, present and future. Nature. 2017;550:345–353. doi:10.1038/nature24286.
11. Doludin Y V., Borisova AL, Pokrovskaya MS, et al. Current best practices and biobanking recommendations. Russ Clin Lab Diagnostics. 2019;64:769–776. (In Russ.) doi:10.18821/0869-2084-2019-64-12-769-776.
12. Anisimov S.V., Glotov A.S., Granstrem O.K. et al. Biobanks and biomedical progress. St.Petersburg: Svoe izdatel'stvo. 2018; 86. (In Russ.)
13. Anisimov S V., Meshkov AN, Glotov AS, et al. National Association of Biobanks and Biobanking Specialists: New Community for Promoting Biobanking Ideas and Projects in Russia. Biopreserv Biobank. 2020;00. doi:10.1089/bio.2020.0049.
14. Nasarabadi S, Hogan M, Nelson J. Biobanking in Precision Medicine. Curr Pharmacol Reports. 2018;4:91–101. doi:10.1007/s40495-018-0123-8.
15. Gillespie K, Luft H, Hernandez Y, et al. Patient Views on the Use of Personal Health Information and Biological Samples for Biobank Research. J Patient-Centered Res Rev. 2017;4:171. doi:10.17294/2330-0698.1516.
16. Gaziano JM, Concato J, Brophy M, et al. Million Veteran Program: A mega-biobank to study genetic influences on health and disease. J Clin Epidemiol. 2016;70:214–223. doi:10.1016/j.jclinepi.2015.09.016.
17. Chen WC, Kerr R, May A, et al. The Integrity and Yield of Genomic DNA Isolated from Whole Blood Following Long-Term Storage at -30°C. Biopreserv Biobank. 2018;16:106–113. doi:10.1089/bio.2017.0050.
18. Bulla A, De Witt B, Ammerlaan W, et al. Blood DNA Yield but Not Integrity or Methylation Is Impacted after Long-Term Storage. Biopreserv Biobank. 2016;14:29–38. doi:10.1089/bio.2015.0045.
19. Björkesten J, Enroth S, Shen Q, et al. Stability of Proteins in Dried Blood Spot Biobanks. Mol Cell Proteomics. 2017;16:1286–1296. doi:10.1074/mcp.RA117.000015.
20. Ferro P, Ortega-Pinazo J, Martínez B, et al. On the Use of Buffy or Whole Blood for Obtaining DNA of High Quality and Functionality: What Is the Best Option? Biopreserv Biobank. 2019;17:577–582. doi:10.1089/bio.2019.0024.
21. Bycroft C, Freeman C, Petkova D, et al. The UK Biobank resource with deep phenotyping and genomic data. Nature. 2018;562:203–209. doi:10.1038/s41586-018-0579-z.
22. Bronkhorst AJ, Aucamp J, Pretorius PJ. Cell-free DNA: Preanalytical variables. Clin Chim Acta. 2015;450:243–253. doi:10.1016/j.cca.2015.08.028.
23. Kang Q, Henry NL, Paoletti C, et al. Comparative analysis of circulating tumor DNA stability In K3EDTA, Streck, and CellSave blood collection tubes. Clin Biochem. 2016;49:1354–1360. doi:10.1016/j.clinbiochem.2016.03.012.
24. Meddeb R, Pisareva E, Thierry AR. Guidelines for the preanalytical conditions for analyzing circulating cell-free DNA. Clin Chem. 2019;65:623–633. doi:10.1373/clinchem.2018.298323.
25. Rubicz R, Zhao S, Wright JL, et al. Gene expression panel predicts metastatic-lethal prostate cancer outcomes in men diagnosed with clinically localized prostate cancer. Mol Oncol. 2017;11:140–150. doi:10.1002/1878-0261.12014.
26. Risberg B, Tsui DWY, Biggs H, et al. Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients. J Mol Diagnostics. 2018;20:883–892. doi:10.1016/j.jmoldx.2018.07.005.
27. Wu WK, Chen CC, Panyod S, et al. Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench. J Formos Med Assoc. 2019;118:545–555. doi:10.1016/j.jfma.2018.02.005.
28. Fouhy F, Deane J, Rea MC, et al. The effects of freezing on faecal microbiota as determined using miseq sequencing and culture-based investigations. Neu J, editor. PLoS One. 2015;10:e0119355. doi:10.1371/journal.pone.0119355.
29. Choo JM, Leong LE, Rogers GB. Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep. 2015;5:16350. doi:10.1038/srep16350.
30. Tedjo DI, Jonkers DMAE, Savelkoul PH, et al. The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects. Favia G, editor. PLoS One. 2015;10:e0126685. doi:10.1371/journal.pone.0126685.
31. Reck M, Tomasch J, Deng Z, et al. Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation. BMC Genomics. 2015;16:494. doi:10.1186/s12864-015-1694-y.
32. Hale VL, Tan CL, Knight R, et al. Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks. J Microbiol Methods. 2015;113:16–26. doi:10.1016/j.mimet.2015.03.021.
33. Sinha R, Chen J, Amir A, et al. Collecting fecal samples for microbiome analyses in epidemiology studies. Cancer Epidemiol Biomarkers Prev. 2016;25:407–416. doi:10.1158/1055-9965.EPI-15-0951.
34. Abrahamson M, Hooker E, Ajami NJ, et al. Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men. Contemp Clin Trials Commun. 2017;7:158–162. doi:10.1016/j.conctc.2017.07.002.
35. Anderson EL, Li W, Klitgord N, et al. A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome. Sci Rep. 2016;6:31731. doi:10.1038/srep31731.
36. Jha AR, Davenport ER, Gautam Y, et al. Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol. 2018;16:1–30. doi:10.1371/journal.pbio.2005396.
37. Ma Y, Chen H, Lei R, et al. Biobanking for human microbiome research: promise, risks, and ethics. Asian Bioeth Rev. 2017;9:311–324. doi:10.1007/s41649-017-0033-9.
38. Ali N, Rampazzo R de CP, Costa ADT, et al. Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. Biomed Res Int. 2017;2017:1–13. doi:10.1155/2017/9306564.
39. Volckmar AL, Sültmann H, Riediger A, et al. A field guide for cancer diagnostics using cell-free DNA: From principles to practice and clinical applications. Genes Chromosom Cancer. 2018;57:123–139. doi:10.1002/gcc.22517.
40. Bag S, Saha B, Mehta O, et al. An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples. Sci Rep. 2016;6:26775. doi:10.1038/srep26775.
41. Lim MY, Song EJ, Kim SH, et al. Comparison of DNA extraction methods for human gut microbial community profiling. Syst Appl Microbiol. 2018;41:151–157. doi:10.1016/j.syapm.2017.11.008.
42. Mackenzie BW, Waite DW, Taylor MW. Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences. Front Microbiol. 2015;6:1–11. doi:10.3389/fmicb.2015.00130.
43. Gerasimidis K, Bertz M, Quince C, et al. The effect of DNA extraction methodology on gut microbiota research applications. BMC Res Notes. 2016;9:365. doi:10.1186/s13104-016-2171-7.
44. Stinson LF, Keelan JA, Payne MS. Comparison of Meconium DNA extraction methods for use in microbiome studies. Front Microbiol. 2018;9:270. doi:10.3389/fmicb.2018.00270.
45. Stadlbauer V, Leber B, Lemesch S, et al. Lactobacillus casei Shirota supplementation does not restore gut microbiota composition and gut barrier in metabolic syndrome: A randomized pilot study. Wong V, editor. PLoS One. 2015;10:e0141399. doi:10.1371/journal.pone.0141399.
46. Hamad I, Ranque S, Azhar EI, et al. Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota. Sci Rep. 2017;7:16788. doi:10.1038/s41598-017-17132-4.
47. Yanagi H, Tsuda A, Matsushima M, et al. Changes in the gut microbiota composition and the plasma ghrelin level in patients with Helicobacter pylori-infected patients with eradication therapy. BMJ Open Gastroenterol. 2017;4:e000182. doi:10.1136/bmjgast-2017-000182.
48. A guide to qualify your clinical samples. Available from: www.findmyassay.com.
49. Trigg RM, Martinson LJ, Parpart-Li S, et al. Factors that influence quality and yield of circulating-free DNA: A systematic review of the methodology literature. Heliyon. 2018;4:e00699. doi:10.1016/j.heliyon.2018.e00699.
50. ISO 20387:2018 Biotechnology - Biobanking - General requirements for biobanking. 2018.