Yeang C H, Ma G C, Hsu H W, Lin Y S, Chang S M, Cheng P J, Chen C A, Ni Y H, Chen M
Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.
Ultrasound Obstet Gynecol. 2014 Jul;44(1):25-30. doi: 10.1002/uog.13377. Epub 2014 Jun 12.
Non-invasive prenatal testing for fetal trisomy 21 (T21) by massively parallel shotgun sequencing (MPSS) is available for clinical use but its efficacy is limited by several factors, e.g. the proportion of cell-free fetal DNA in maternal plasma and sequencing depth. Existing algorithms discard DNA reads from the chromosomes for which testing is not being performed (i.e. those other than chromosome 21) and are thus more susceptible to diluted fetal DNA and limited sequencing depth. We aimed to describe and evaluate a novel algorithm for aneuploidy detection (genome-wide normalized score (GWNS)), which normalizes read counts by the proportions of DNA fragments from chromosome 21 in normal controls.
We assessed the GWNS approach by comparison with two existing algorithms, i.e. Z-score and normalized chromosome value (NCV), using theoretical approximations and computer simulations in a set of 86 cases (64 euploid and 22 T21 cases). We then validated GWNS by studying an expanded set of clinical samples (n = 208). Finally, dilution experiments were undertaken to compare performance of the three algorithms (Z-score, NCV, GWNS) when fetal DNA concentration was low.
At fixed levels of significance and power, GWNS required a smaller fetal DNA proportion and fewer total MPSS reads compared to Z-score or NCV. In dilution experiments, GWNS also outperformed the other two methods by reaching the correct diagnosis with the lowest range of fetal DNA concentrations (GWNS, 3.83-4.75%; Z-score, 4.75-5.22%; NCV, 6.47-8.58%).
Our results demonstrate that GWNS is comparable to Z-score and NCV methods regarding the performance of detecting fetal T21. Dilution experiments suggest that GWNS may perform better than the other methods when fetal fraction is low.
通过大规模平行鸟枪法测序（MPSS）对胎儿21三体（T21）进行无创产前检测已可用于临床，但该检测的有效性受到多种因素限制，例如母血中游离胎儿DNA的比例和测序深度。现有算法会舍弃来自未进行检测的染色体（即21号染色体以外的染色体）的DNA读数，因此更容易受到稀释的胎儿DNA和有限测序深度的影响。我们旨在描述和评估一种用于非整倍体检测的新算法（全基因组标准化评分（GWNS）），该算法通过正常对照中21号染色体DNA片段的比例对读数计数进行标准化。
我们通过与两种现有算法（即Z评分和标准化染色体值（NCV））进行比较，使用理论近似值和计算机模拟，对86例样本（64例整倍体和22例T21病例）评估GWNS方法。然后，我们通过研究一组扩大的临床样本（n = 208）对GWNS进行验证。最后，进行稀释实验以比较三种算法（Z评分、NCV、GWNS）在胎儿DNA浓度较低时的性能。
在固定的显著性水平和检验效能下，与Z评分或NCV相比，GWNS所需的胎儿DNA比例更小，MPSS总读数更少。在稀释实验中，GWNS在最低胎儿DNA浓度范围内就能得出正确诊断，也优于其他两种方法（GWNS，3.83 - 4.75%；Z评分，4.75 - 5.22%；NCV，6.47 - 8.58%）。
我们的结果表明，在检测胎儿T21的性能方面，GWNS与Z评分和NCV方法相当。稀释实验表明，当胎儿比例较低时，GWNS可能比其他方法表现更好。
