Performance of Streck cfDNA blood collection tubes for liquid biopsy testing

PLoS ONE

Volumn 11, Issue 11, 2016, Pages

  Medina Diaz, Inga ^a   Nocon, Annette ^a   Mehnert, Daniel H ^a   Fredebohm, Johannes ^a   Diehl, Frank ^a   Holtrup, Frank ^a  

^a SYSMEX CORPORATION   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANALYTIC METHOD; ARTICLE; BEAMING; BIOPSY; BLOOD COLLECTION TUBE; COLORECTAL CANCER; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DNA EXTRACTION; DNA FRAGMENTATION; DNA RELEASE; GENE MUTATION; GENETIC ANALYSIS; GENETIC PARAMETERS; GENETIC STABILITY; GENOMIC DNA LEVEL; HUMAN; LIQUID BIOPSY TESTING; MUTANT; MUTATION RATE; PLASMA SAFE SEQUENCING; PLASMA VOLUME; POLYMERASE CHAIN REACTION; ROOM TEMPERATURE; STORAGE TEMPERATURE; TREATMENT DURATION; WILD TYPE; BLOOD; BLOOD SAMPLING; COLORECTAL TUMOR; DEVICES; DNA MUTATIONAL ANALYSIS; GENETICS; ISOLATION AND PURIFICATION; MUTATION; PROCEDURES; TEMPERATURE;

BLOOD SPECIMEN COLLECTION; COLORECTAL NEOPLASMS; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; HUMANS; MUTATION; TEMPERATURE;

EID: 84994707439     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0166354     Document Type: Article

References (34)

1. Crowley E, Di Nicolantonio F, Loupakis F, Bardelli A. Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013; 10: 472-484. doi: 10.1038/nrclinonc.2013.110 PMID: 23836314
2. Diaz LA, Bardelli A. Liquid Biopsies: Genotyping Circulating Tumor DNA. J Clin Oncol. 2014; 32. doi: 10.1200/JCO.2012.45.2011 PMID: 24449238
3. Bronkhorst AJ, Aucamp J, Pretorius PJ. Cell-free DNA: Preanalytical variables. Clin Chim Acta. Elsevier B.V.; 2015; 450: 243-53. doi: 10.1016/j.cca.2015.08.028 PMID: 26341895
4. Tu M, Chia D, Wei F, Wong D. Liquid biopsy for detection of actionable oncogenic mutations in human cancers and electric field induced release and measurement liquid biopsy (eLB). Analyst. 2016; 141: 393-402. doi: 10.1039/c5an01863c PMID: 26645892
5. Sherwood JL, Corcoran C, Brown H, Sharpe AD, Musilova M, Kohlmann A. Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC). PLoS One. 2016; 11: e0150197. doi: 10.1371/journal.pone.0150197 PMID: 26918901
6. El Messaoudi S, Rolet F, Mouliere F, Thierry AR. Circulating cell free DNA: Preanalytical considerations. Clin Chim Acta. 2013; 424: 222-30. doi: 10.1016/j.cca.2013.05.022 PMID: 23727028
7. Malentacchi F, Pizzamiglio S, Verderio P, Pazzagli M, Orlando C, Ciniselli CM, et al. Influence of storage conditions and extraction methods on the quantity and quality of circulating cell-free DNA (ccfDNA): the SPIDIA-DNAplas External Quality Assessment experience. Clin Chem Lab Med. 2015; 53: 1935-42. doi: 10.1515/cclm-2014-1161 PMID: 25883202
8. Fleischhacker M, Schmidt B, Weickmann S, Fersching DMI, Leszinski GS, Siegele B, et al. Methods for isolation of cell-free plasma DNA strongly affect DNA yield. Clin Chim Acta. 2011; 412: 2085-8. doi: 10.1016/j.cca.2011.07.011 PMID: 21861994
9. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014; 6: 224ra24. doi: 10.1126/scitranslmed.3007094 PMID: 24553385
10. Diehl F, Schmidt K, Choti M a, Romans K, Goodman S, Li M, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008; 14: 985-90. doi: 10.1038/nm.1789 PMID: 18670422
11. Toro PV, Erlanger B, Beaver J a, Cochran RL, VanDenBerg D a, Yakim E, et al. Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA. Clin Biochem. Elsevier B.V.; 2015; 48: 993-8. doi: 10.1016/j.clinbiochem.2015.07.097 PMID: 26234639
12. Das K, Fernando MR, Basiaga S, Wigginton SM, Williams T. Effects of a novel cell stabilizing reagent on DNA amplification by PCR as compared to traditional stabilizing reagents. Acta Histochem. Elsevier GmbH.; 2013; doi: 10.1016/j.acthis.2013.05.002 PMID: 23810682
13. Streck. Cell-Free DNA BCT: INSTRUCTIONS FOR USE. Omaha, NE, USA; 2014.
14. Lo YMD, Chiu RWK. Genomic Analysis of Fetal Nucleic Acids in Maternal Blood. Annu Rev Genomics Hum Genet. 2012; 13: 285-306. doi: 10.1146/annurev-genom-090711-163806 PMID: 22657389
15. Kang Q, Henry NL, Paoletti C, Jiang H, Vats P, Chinnaiyan AM, et al. Comparative Analysis of Circulating Tumor DNA Stability In K3EDTA, Streck and CellSave Blood Collection Tubes. Clin Biochem. Elsevier B.V.; 2016; doi: 10.1016/j.clinbiochem.2016.03.012 PMID: 27129799
16. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A. 2011; 108: 9530-5. doi: 10.1073/pnas.1105422108 PMID: 21586637
17. Rago C, Huso DL, Diehl F, Karim B, Liu G, Papadopoulos N, et al. Serial assessment of human tumor burdens in mice by the analysis of circulating DNA. Cancer Res. 2007; 67: 9364-70. doi: 10.1158/0008-5472.CAN-07-0605 PMID: 17909045
18. Jiang P, Lo YMD. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics. Trends Genet. Elsevier Ltd; 2016; 32: 360-371. doi: 10.1016/j.tig.2016.03.009 PMID: 27129983
19. Mouliere F, Robert B, Peyrotte E, Del Rio M, Ychou M, Molina F, et al. High fragmentation characterizes tumour-derived circulating DNA. PLoS One. 2011;6. doi: 10.1371/journal.pone.0023418 PMID: 21909401
20. Diehl F, Li M, He Y, Kinzler KW, Vogelstein B, Dressman D. BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nat Methods. 2006; 3: 551-559. doi: 10.1038/NMETH898 PMID: 16791214
21. Wong D, Moturi S, Angkachatchai V, Mueller R, Desantis G, van den Boom D, et al. Optimizing blood collection, transport and storage conditions for cell free DNA increases access to prenatal testing. Clin Biochem. The Authors; 2013; 46: 1099-1104. doi: 10.1016/j.clinbiochem.2013.04.023 PMID: 23643886
22. Devonshire AS, Whale AS, Gutteridge A, Jones G, Cowen S, Foy CA, et al. Towards standardisation of cell-free DNA measurement in plasma: Controls for extraction efficiency, fragment size bias and quantification. Anal Bioanal Chem. 2014; 406: 6499-6512. doi: 10.1007/s00216-014-7835-3 PMID: 24853859
23. Chan KCA, Yeung S-W, Lui W-B, Rainer TH, Lo YMD. Effects of preanalytical factors on the molecular size of cell-free DNA in blood. Clin Chem. 2005; 51: 781-784.
24. Karlsen F, Kalantari M, Chitemerere M, Johansson B, Hagmar B. Modifications of human and viral deoxyribonucleic acid by formaldehyde fixation. Lab Invest. 1994; 71: 604-611. PMID: 7967515
25. Neil DO, Schroeer S, Luo Y, Sperling T. A new method for DNA extraction and artifact removal from FFPE samples for next-generation sequencing experiments Sample & Assay Technologies. 2014; 40724.
26. Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A. 2005; 102: 16368-73. doi: 10.1073/pnas.0507904102 PMID: 16258065
27. Thierry AR, Mouliere F, El Messaoudi S, Mollevi C, Lopez-Crapez E, Rolet F, et al. Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA. Nat Med. 2014; 20: 430-5. doi: 10.1038/nm.3511 PMID: 24658074
28. Jones F, Dan E, Wichner K, Ross C, Stieler K, Boehm V, et al. Performance of standardized BEAMing platform for detecting RAS mutations in the blood of metastatic colorectal cancer (mCRC) patients. 2016. p. J Clin Oncol 34, 2016 (suppl; abstr 11538).
29. Fernando MR, Chen K, Norton S, Krzyzanowski G, Bourne D, Hunsley B, et al. A new methodology to preserve the original proportion and integrity of cell-free fetal DNA in maternal plasma during sample processing and storage. Prenat Diagn. 2010; 30: 418-424. PMID: 20306459
30. Norton SE, Lechner JM, Williams T, Fernando MR. A stabilizing reagent prevents cell-free DNA contamination by cellular DNA in plasma during blood sample storage and shipping as determined by digital PCR. Clin Biochem. The Authors; 2013; 46: 1561-5. doi: 10.1016/j.clinbiochem.2013.06.002 PMID: 23769817
31. Norton SE, Luna KK, Lechner JM, Qin J, Fernando MR. A New Blood Collection Device Minimizes Cellular DNA Release During Sample Storage and Shipping When Compared to a Standard Device. J Clin Lab Anal. 2013; 27: 305-311. doi: 10.1002/jcla.21603 PMID: 23852790
32. Hidestrand M, Stokowski R, Song K, Oliphant A, Deavers J, Goetsch M, et al. Influence of Temperature during Transportation on Cell-Free DNA Analysis. Fetal Diagn Ther. 2012; 31: 122-128. doi: 10.1159/000335020 PMID: 22261730
33. Chan KCA, YeungS-W, Lui W-B, Rainer TH, Lo YMD. Effects of preanalytical factors on the molecular size of cell-free DNA in blood. Clin Chem. 2005; 51: 781-4. doi: 10.1373/clinchem.2004.046219 PMID: 15708950
34. Distler J, Tetzner R, Weiss G, König T, Schlegel A, Bagrowski M. Evaluation of different blood collection tubes and blood storage conditions for the preservation and stability of cell-free circulating DNA for the analysis of the methylated mSEPT9 colorectal cancer screening marker. P 209. Berlin; 2015. p. 69. Available: http://www.cnaps-congress.com/-static/media/CNAPS-2015-Programm-A4-PP-web.pdf