Prospective chromosome analysis of 3429 amniocentesis samples in China using copy number variation sequencing
Prospective chromosome analysis of 3429 amniocentesis samples in China using copy number variation sequencing
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DOI：
10.1016/j.ajog.2018.05.030
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发表时间：
2018-09-01
影响因子：
9.8
通讯作者：
Liu, Hongqian
中科院分区：
文献类型：
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作者：
Wang, Jing;Chen, Lin;Liu, Hongqian
背景技术背景：下一代测序技术正在成为染色体微阵列分析的一种可行的替代方法，用于诊断染色体疾病综合征。一种下一代测序方法，拷贝数变异测序，已被证明提供高可靠性，准确性和重现性，用于检测产前样品中的胎儿拷贝数变异。然而，它作为一个第一层诊断方法的临床实用性还有待于在一个大的孕妇队列中进行胎儿染色体检测。目的：我们试图评估拷贝数变异测序作为一个第一层诊断方法，用于检测具有高危产前指征的孕妇的一般人群中的胎儿染色体异常。这是一项对3429名因不同风险指征（包括高龄产妇、高危产妇血清筛查和超声软标记物阳性）而接受子宫颈穿刺术和胎儿染色体检测的孕妇进行的前瞻性分析。通过标准程序进行羊膜穿刺术。通过拷贝数变异测序分析羊膜细胞DNA，染色体分辨率为0.1 Mb。胎儿染色体异常，包括整个染色体非整倍体和节段不平衡的金标准的细胞遗传学和分子方法和其致病性确定以下指南的美国医学遗传学学院的序列variants.RESULTS：明确的可解释的拷贝数变异测序结果，获得所有3429个穿刺样本。拷贝数变异测序鉴定出3293个样本（96%）具有正常的分子核型，136个样本（4%）具有改变的分子核型。共检测到146例胎儿染色体异常，包括46例全染色体非整倍性（致病性），29例已知或疑似与染色体疾病综合征相关的亚显微镜微缺失/微重复（致病性），22例其他微缺失/微重复（可能致病性）和49例意义不明的变异体。总体而言，患者队列中致病性/可能致病性和不确定意义的染色体异常变体的累积频率分别为2.83%和1.43%。在高危高龄孕妇、高危孕妇血清筛查、超声软标记3组中，检出的全染色体非整倍体最多的是21三体，其次是性染色体非整倍体、18三体、13三体。在所有临床适应症中，亚显微镜下拷贝数变异的发生率相似，致病性/可能致病性和不确定意义拷贝数变异的变异体的比例大致相等。如果核型分析已被用作一种替代的细胞遗传学检测方法，拷贝数变异测序将返回一个1%的高产量的致病性或可能致病的拷贝数variations.CONCLUSION：在一个大型的前瞻性临床研究，拷贝数变异测序提供了高可靠性和准确性，用于确定临床显着的胎儿异常产前样本。基于关键性能标准，拷贝数变异测序似乎是一种非常适合的方法，用于一般人群中有疑似胎儿染色体异常风险的孕妇的一级诊断。
BACKGROUND: Next-generation sequencing is emerging as a viable alternative to chromosome microarray analysis for the diagnosis of chromosome disease syndromes. One next-generation sequencing methodology, copy number variation sequencing, has been shown to deliver high reliability, accuracy, and reproducibility for detection of fetal copy number variations in prenatal samples. However, its clinical utility as a first-tier diagnostic method has yet to be demonstrated in a large cohort of pregnant women referred for fetal chromosome testing.OBJECTIVE: We sought to evaluate copy number variation sequencing as a first-tier diagnostic method for detection of fetal chromosome anomalies in a general population of pregnant women with high-risk prenatal indications.STUDY DESIGN: This was a prospective analysis of 3429 pregnant women referred for amniocentesis and fetal chromosome testing for different risk indications, including advanced maternal age, high-risk maternal serum screening, and positivity for an ultrasound soft marker. Amniocentesis was performed by standard procedures. Amniocyte DNA was analyzed by copy number variation sequencing with a chromosome resolution of 0.1 Mb. Fetal chromosome anomalies including whole chromosome aneuploidy and segmental imbalances were independently confirmed by gold standard cytogenetic and molecular methods and their pathogenicity determined following guidelines of the American College of Medical Genetics for sequence variants.RESULTS: Clear interpretable copy number variation sequencing results were obtained for all 3429 amniocentesis samples. Copy number variation sequencing identified 3293 samples (96%) with a normal molecular karyotype and 136 samples (4%) with an altered molecular karyotype. A total of 146 fetal chromosome anomalies were detected, comprising 46 whole chromosome aneuploidies (pathogenic), 29 submicroscopic microdeletions/microduplications with known or suspected associations with chromosome disease syndromes (pathogenic), 22 other microdeletions/microduplications (likely pathogenic), and 49 variants of uncertain significance. Overall, the cumulative frequency of pathogenic/likely pathogenic and variants of uncertain significance chromosome anomalies in the patient cohort was 2.83% and 1.43%, respectively. In the 3 high-risk advanced maternal age, high-risk maternal serum screening, and ultrasound soft marker groups, the most common whole chromosome aneuploidy detected was trisomy 21, followed by sex chromosome aneuploidies, trisomy 18, and trisomy 13. Across all clinical indications, there was a similar incidence of submicroscopic copy number variations, with approximately equal proportions of pathogenic/likely pathogenic and variants of uncertain significance copy number variations. If karyotyping had been used as an alternate cytogenetics detection method, copy number variation sequencing would have returned a 1% higher yield of pathogenic or likely pathogenic copy number variations.CONCLUSION: In a large prospective clinical study, copy number variation sequencing delivered high reliability and accuracy for identifying clinically significant fetal anomalies in prenatal samples. Based on key performance criteria, copy number variation sequencing appears to be a well-suited methodology for first-tier diagnosis of pregnant women in the general population at risk of having a suspected fetal chromosome abnormality.