Diagnostic Detection of Allelic Losses and Imbalances by Next-Generation Sequencing 1p/19q Co-Deletion Analysis of Gliomas
Diagnostic Detection of Allelic Losses and Imbalances by Next-Generation Sequencing 1p/19q Co-Deletion Analysis of Gliomas
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DOI：
10.1016/j.jmoldx.2016.06.002
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发表时间：
2016-09-01
影响因子：
4.1
通讯作者：
Dinjens, Winand N. M.
中科院分区：
文献类型：
--
作者：
Dubbink, Hendrikus J.;Atmodimedjo, Peggy N.;Dinjens, Winand N. M.
癌细胞是基因组不稳定的，并积累肿瘤类型特异性分子畸变，这可能是预测预后和治疗靶点的标志。染色体1p和19q的共缺失标志着胶质瘤具有少突胶质细胞瘤成分，预示着更好的预后和对化疗的反应。在目前的研究中，我们提出了一种在诊断环境中检测染色体1p/19q共缺失或杂合性缺失（LOH）的新方法，基于单核苷酸多态性（SNP）分析和下一代测序（NGS）。我们选择高度多态的snp均匀分布在两条染色体臂上。为了实验确定靶向SNP分析的敏感性和特异性，我们从49例常规福尔马林固定石蜡包埋胶质瘤组织中提取dna，并将结果与基于诊断微卫星的LOH分析和计算估计值进行比较。我们发现，根据计算结果，NGS的靶向SNP分析可以在70%的正常细胞背景下可靠地检测到1p和/或19q缺失，比基于微卫星的LOH分析更敏感，并且需要更少的DNA。这种特异且敏感的SNP分析广泛适用于多个基因组区域的同时等位基因失衡分析，并且可以很容易地纳入NGS突变分析。结合突变和染色体不平衡分析在一个单一的NGS分析是非常适合常规胶质瘤诊断和其他诊断分子病理学应用。
Cancer cells are genomically unstable and accumulate tumor type-specific molecular aberrations, which may represent hallmarks for predicting prognosis and targets for therapy. Co-deletion of chromosomes 1p and 19q marks gliomas with an oligodendroglioma component and predicts a better prognosis and response to chemotherapy. In the current study, we present a novel method to detect chromosome 1p/19q co-deletion or loss of heterozygosity (LOH) in a diagnostic setting, based on single-nucleotide polymorphism (SNP) analysis and next-generation sequencing (NGS). We selected highly polymorphic SNPs distributed evenly over both chromosome arms. To experimentally determine the sensitivity and specificity of targeted SNP analysis, we used DNAs extracted from 49 routine formalin-fixed, paraffin embedded glioma tissues and compared the outcome with diagnostic microsatellite-based LOH analysis and calculated estimates. We show that targeted SNP analysis by NGS allows reliable detection of 1p and/or 19q deletion in a background of 70 % of normal cells according to calculated outcomes, is more sensitive than microsatellite-based LOH analysis, and requires much Less DNA. This specific and sensitive SNP assay is broadly applicable for simultaneous allelic imbalance analysis of multiple genomic regions and can be incorporated easily into NGS mutation analyses. The combined mutation and chromosomal imbalance analysis in a single NGS assay is suited perfectly for routine glioma diagnostics and other diagnostic molecular pathology applications.