Circulating free DNA in the era of precision oncology: Pre‐ and post‐analytical concerns

Chronic Diseases and Translational Medicine - Tập 2 - Trang 223-230 - 2016
Jun-Liang Lu1, Zhi-Yong Liang1
1Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China

Tóm tắt

AbstractCancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the onset of secondary resistance, and relapse. Circulating free DNA (cfDNA) has emerged as an ideal source of genetic information for cancer patients, and numerous studies have explored its validity in various clinical applications. However, clinical implementation of cfDNA‐based tests has been slow. In this review, we addressed some of the pre‐ and post‐analytical issues regarding cfDNA tests. First, we summarized the characteristics of cfDNA and reviewed the methods used to identify tumor‐derived cfDNA from the pool of total cfDNA. Second, we described the procedures used to extract cfDNA, which have a great impact on representativeness and yield. Finally, we discussed our thoughts on the validation of cfDNA‐based tests and the reporting of test results amid drastic limitations.

Tài liệu tham khảo

10.1053/j.seminhematol.2010.07.001 10.1200/JCO.2003.10.038 10.1056/NEJMoa044238 10.1200/JCO.2010.33.4235 10.1056/NEJMp1500523 10.1038/nm0313-249 10.3389/fgene.2016.00060 National Research Council (US) Committee on A Framework for Developing a New Taxonomy of Disease, 2011, Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease 10.1371/journal.pone.0161012 Jahr S., 2001, DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells, Cancer Res, 61, 1659 Zhivotosky B., 2001, Assessment of apoptosis and necrosis by DNA fragmentation and morphological criteria, 10.1002/0471143030.cb1803s12 10.1016/S0009-8981(01)00665-9 10.18632/oncotarget.6874 10.1371/journal.pone.0108247 10.1097/JTO.0b013e3182307f98 10.1373/clinchem.2016.257469 10.1038/srep31985 10.1158/1078-0432.CCR-15-2470 10.1038/nm.1789 Wu Y.L., 2016, Liquid biopsy: specification with precision, J Evid Based Med, 16, 193 10.1111/bju.13586 10.1007/s00428-016-2004-z List of Cleared or Approved Companion Diagnostic Devices (In Vitro and Imaging Tools).http://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm301431.htm. Updated October 28 2016. Accessed December 1 2016. 10.1186/s40880-016-0092-4 10.1038/nrc3066 10.3390/ijms140918925 10.1634/theoncologist.2016-0082 10.1038/nm.3519 10.1016/j.tig.2015.02.001 10.1158/2159-8290.CD-15-0344 10.1371/journal.pcbi.1004731 10.1007/978-94-017-7484-0 10.2196/resprot.6024 10.1186/s13058-016-0696-2 10.1158/2159-8290.CD-15-1283 10.1038/nature08658 10.1530/ERC-15-0369 10.1073/pnas.1519286113 10.1373/clinchem.2015.253609 10.1016/j.ebiom.2015.08.015 10.1371/journal.pgen.1006162 10.1073/pnas.1500076112 10.1073/pnas.1501321112 10.1371/journal.pone.0023418 10.1182/blood-2013-02-485771 10.1093/clinchem/48.10.1647 10.1101/gr.192294.115 10.1016/j.cell.2015.11.050 10.1126/sciadv.1500734 10.1021/nl3039162 10.1517/14712598.2012.673577 Korabecna M., 2011, Circulating Nucleic Acids in Plasma and Serum: Proceedings of the 6th International Conference on Circulating Nucleic Acids in Plasma and Serum Held on 9–11 November 2009 in Hong Kong, 195 10.1373/clinchem.2003.026013 10.1016/j.clinbiochem.2016.03.012 10.1371/journal.pone.0025202 10.1016/j.cca.2015.08.028 10.1016/j.dib.2015.12.009 10.1515/cclm-2014-1161 10.3349/ymj.2012.53.1.132 10.1016/j.cca.2011.07.011 10.1007/978-3-319-42044-8_33 10.1371/journal.pone.0077963 10.1016/j.jchromb.2006.04.026 Ford A., 2015, Next‐generation liquid biopsy: tumor monitoring from droplet volumes of blood, J Cancer Prev Curr Res, 3, 00064 10.1016/j.cca.2009.02.018 Parpart‐Li ST Bartlett B Popoli M et al.The effect of preservative and temperature on the analysis of circulating tumor DNA[published online ahead of print November 8 2016].Clin Cancer Res. doi:10.1158/1078‐0432.CCR‐16‐1691. 10.1371/journal.pone.0150197 10.1016/j.biomaterials.2016.06.003 10.1200/JCO.2006.05.9493 10.1371/journal.pone.0087838 10.1136/jclinpath-2014-202404 ISO/TC 212ISO 15189:2012.Medical Laboratories—Requirements for Quality and Competence.2012 ISO/CASCOISO/IEC 17025:2005.General Requirements for the Competence of Testing and Calibration Laboratories.2005 10.1016/j.jcv.2012.11.013 10.1038/ejhg.2010.101 10.1038/nbt.2696 10.1038/nm.3511 10.1007/s00216-014-7835-3 Duan H., 2015, Comparison of EGFR mutation status between plasma and tumor tissue in non‐small cell lung cancer using the Scorpion ARMS method and the possible prognostic significance of plasma EGFR mutation status, Int J Clin Exp Pathol, 8, 13136 10.1038/srep06269 Chae YK Davis AA Carneiro BA.Concordance between genomic alterations assessed by next‐generation sequencing in tumor tissue or circulating cell‐free DNA[published online ahead of print August 30 2016].Oncotarget. doi:10.18632/oncotarget.11692. 10.1056/NEJMsb1607705