Institute of Human Genetics.
Institute of Molecular Biotechnology, Technical University of Graz, Graz, Austria.
Clin Chem. 2015 Jun;61(6):838-49. doi: 10.1373/clinchem.2014.234286. Epub 2015 Apr 20.
Recent progress in the analysis of cell-free DNA fragments [cell-free circulating tumor DNA (ctDNA)] now allows monitoring of tumor genomes by noninvasive means. However, previous studies with plasma DNA from patients with cancer demonstrated highly variable allele frequencies of ctDNA. The comprehensive analysis of tumor genomes is greatly facilitated when plasma DNA has increased amounts of ctDNA. Therefore, a fast and cost-effective prescreening method to identify such plasma samples without previous knowledge about alterations in the respective tumor genome could assist in the selection of samples suitable for further extensive qualitative analysis.
We adapted the recently described Fast Aneuploidy Screening Test-Sequencing System (FAST-SeqS) method, which was originally established as a simple, effective, noninvasive screening method for fetal aneuploidy from maternal blood.
We show that our modified FAST-SeqS method (mFAST-SeqS) can be used as a prescreening tool for an estimation of ctDNA percentage. With a combined evaluation of genome-wide and chromosome arm-specific z-scores from dilution series with cell line DNA and by comparisons of plasma-Seq profiles with data from mFAST-SeqS, we established a detection limit of ≥10% mutant alleles. Plasma samples with an mFAST-SeqS z-score >5 showed results that were highly concordant with those of copy number profiles obtained from our previously described plasma-Seq approach.
Advantages of this approach include the speed and cost-effectiveness of the assay and that no prior knowledge about the genetic composition of tumor samples is necessary to identify plasma DNA samples with >10% ctDNA content.
游离 DNA 片段[游离循环肿瘤 DNA（ctDNA）]分析的最新进展现在允许通过非侵入性手段监测肿瘤基因组。然而，来自癌症患者血浆 DNA 的先前研究表明 ctDNA 的等位基因频率变化很大。当血浆 DNA 具有更多的 ctDNA 时，对肿瘤基因组进行全面分析会更加方便。因此，一种快速且具有成本效益的预筛选方法，可以在没有关于相应肿瘤基因组改变的先验知识的情况下识别此类血浆样本，可以帮助选择适合进一步进行广泛定性分析的样本。
我们对最近描述的快速非整倍体筛选测试测序系统（FAST-SeqS）方法进行了改编，该方法最初作为一种从母体血液中简单、有效、非侵入性的胎儿非整倍体筛选方法而建立。
我们表明，我们修改的 FAST-SeqS 方法（mFAST-SeqS）可用作 ctDNA 百分比估计的预筛选工具。通过对来自细胞系 DNA 的稀释系列的全基因组和染色体臂特异性 z 分数的综合评估，并通过与 mFAST-SeqS 的血浆测序图谱的比较，我们建立了≥10%突变等位基因的检测限。mFAST-SeqS z 分数>5 的血浆样本的结果与我们之前描述的血浆测序方法获得的拷贝数图谱高度一致。
该方法的优点包括检测的速度和成本效益，并且无需事先了解肿瘤样本的遗传组成即可识别具有>10%ctDNA 含量的血浆 DNA 样本。
