Evaluation of commercial kits for purification of circulating free DNA

被引:99
作者
Diefenbach, Russell J. [1 ,3 ]
Lee, Jenny H. [1 ,3 ]
Kefford, Richard F. [2 ,3 ,4 ,5 ]
Rizos, Helen [1 ,3 ]
机构
[1] Macquarie Univ, Fac Med & Hlth Sci, Dept Biomed Sci, Sydney, NSW 2109, Australia
[2] Macquarie Univ, Fac Med & Hlth Sci, Dept Clin Med, Sydney, NSW 2109, Australia
[3] Melanoma Inst Australia, Poche Ctr, St Leonards, NSW 2065, Australia
[4] Westmead Hosp, Crown Princess Mary Canc Ctr, Dept Med Oncol, Sydney, NSW 2145, Australia
[5] Blacktown Hosp, Crown Princess Mary Canc Ctr, Dept Med Oncol, Sydney, NSW 2145, Australia
基金
英国医学研究理事会;
关键词
Circulating free DNA; Circulating tumor DNA; Liquid biopsy; Biomarker; CELL-FREE-DNA; BLOOD COLLECTION TUBES; TUMOR DNA; CANCER-PATIENTS; LIQUID BIOPSY; ORIGIN; QUANTIFICATION; RESISTANCE; PLASMA; CTDNA;
D O I
10.1016/j.cancergen.2018.08.005
中图分类号
R73 [肿瘤学];
学科分类号
100214 ;
摘要
Analysis of liquid biopsies and the identification of non-invasive biomarkers for the diagnosis and prognosis of solid tumors has grown exponentially over the last few years. This has led to an increasing number of commercial kits optimised for the purification of circulating free (cf) DNA and RNA/miRNA from biofluids such as plasma, serum and urine. To optimise and standardise current practices we sought to evaluate the performance of spin column-based and magnetic bead-based commercial kits. The following commercial cfDNA purification kits were analysed in this study: QlAamp circulating nucleic acid kit (Qiagen, Germany); Plasma/serum cell-free circulating DNA Purification midi kit (Norgen Biotek, Canada); QIAamp minElute ccfDNA mini kit (Qiagen); Maxwell RSC ccfDNA plasma kit (Promega, USA); MagMAX cell-free DNA isolation kit (Applied Biosystems, USA); and NextPrep-Mag cfDNA isolation kit (Bioo Scientific, USA). Extracted DNA from the plasma of healthy individuals, either nonspiked or spiked with DNA fragments or cfDNA, was evaluated for recovery using either a BioRad Experion or ddPCR analysis. This study represents the first to use a comprehensive size distribution of spiked-in DNA fragments to evaluate commercial cfDNA kits. The commonly used spin column-based Qiagen QlAamp circulating nucleic acid kit was found to be the most consistent performing kit across the two evaluation assays employed. The Qiagen QlAamp minElute ccfDNA mini kit represented the best performing magnetic bead-based kit and provides an alternative based on lower cost/sample with a simpler workflow than spin column-based kits.
引用
收藏
页码:21 / 27
页数:7
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