High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions.
High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions.
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DOI：
10.1371/journal.pone.0153182
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Peters DG
中科院分区：
文献类型：
--
作者：
Chu T;Yeniterzi S;Yatsenko SA;Dunkel M;Shaw PA;Bunce KD;Peters DG
我们的目的是验证这样一种假设，即通过基于序列的母体血浆DNA分析，在无创产前检测胎儿微缺失时，对照样本中个体间基因组拷贝数变异是一个混杂因素。使用基因组变异数据库（DGV）确定人类基因组中每个50kb区域的“基因组变异频率”（GVF）。对15份核型正常母体血浆和6份CVS DNA对照样本进行全基因组测序。这些样本的相对读计数变异系数（cv.RTC）被确定为每个50kb区域。我们还对两例5p染色体微缺失孕妇的血浆进行了测序，并使用GCREM算法进行了分析。我们发现，在对照组中，读取计数的高方差与GVF之间存在很强的相关性。因此，我们无法通过从两个连续受影响的妊娠中获得的母体血浆样本测序来确认微缺失的存在。在为微删除执行NIPT时应该谨慎。发展我们对影响这些方法的敏感性和特异性的因素的理解是至关重要的。特别是，对照间良性拷贝数变异是一个主要的混杂因素，它们的影响应该通过生物信息学加以纠正。
Our goal was to test the hypothesis that inter-individual genomic copy number variation in control samples is a confounding factor in the non-invasive prenatal detection of fetal microdeletions via the sequence-based analysis of maternal plasma DNA. The database of genomic variants (DGV) was used to determine the “Genomic Variants Frequency” (GVF) for each 50kb region in the human genome. Whole genome sequencing of fifteen karyotypically normal maternal plasma and six CVS DNA controls samples was performed. The coefficient of variation of relative read counts (cv.RTC) for these samples was determined for each 50kb region. Maternal plasma from two pregnancies affected with a chromosome 5p microdeletion was also sequenced, and analyzed using the GCREM algorithm. We found strong correlation between high variance in read counts and GVF amongst controls. Consequently we were unable to confirm the presence of the microdeletion via sequencing of maternal plasma samples obtained from two sequential affected pregnancies. Caution should be exercised when performing NIPT for microdeletions. It is vital to develop our understanding of the factors that impact the sensitivity and specificity of these approaches. In particular, benign copy number variation amongst controls is a major confounder, and their effects should be corrected bioinformatically.