Comparison of Prenatal Bacterial Artificial Chromosome Microspheres (BoBs) and High-throughput Sequencing Copy Number Variation (CNV-seq) Detection Techniques in Prenatal Diagnosis
2020.11.05

Annoroad jointly explored the application of BoBs and CNV-seq in prenatal diagnosis with Xu Liangpu team of Maternity and Child Care Centers in Fujian Province. The research results - TThe Comprehensive Comparison of Bacterial Artificial Chromosomes (BACs)-on-Beads Assay and Copy Number Variation Sequencing in Prenatal Diagnosis of Southern Chinese Women (comprehensive comparison of bacterial artificial chromosome detection and copy number variation sequencing in prenatal diagnosis of pregnant women in southern China) was published on November 1, 2020 in the Journal of Molecular Diagnostics (IF: 5.553, JCR Q1), a journal of Elsevier Press.


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Chromosomal abnormalities refer to changes in the number and structure of chromosomes, which can lead to congenital malformations, fetal growth restrictions, mental retardation, abortion and other adverse consequences. Up to now, more than 200 syndromes caused by chromosomal abnormalities have been found, and there is no effective treatment. Therefore, prenatal diagnosis of chromosomal abnormalities is particularly important to prevent birth defects.

The traditional clinical prenatal diagnosis method is to detect fetal chromosomes through karyotyping technology, but due to technical limitations, this method cannot identify microdeletion, microduplications and other chromosome copy number variations (CNV), which often leads to missed diagnosis.

Bacterial Artificial Chromosomes (BACs)-on-Beads (BoBs) and CNV-seq technology based on high-throughput sequencing are two new prenatal diagnostic methods that have emerged in recent years. With accurate test results and low test cost, they have been accepted by clinic gradually and started to be applied on a large scale.

Although a number of studies have tested the detection performance of BoBs and CNV-seq in various aspects, so far, the two methods have not been directly compared, so there is still a lack of clinical evidence on how to choose between the two techniques in prenatal diagnosis.

A total of 1,876 samples of amniotic fluid and umbilical cord blood collected from pregnant women during prenatal diagnosis in Maternity and Child Care Centers in Fujian Province between November 2015 and February 2019 were included in the study.


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Each sample was divided into several copies for karyotype analysis, BoBs testing, and CNV-seq analysis. Samples with inconsistent results of pathogenic CNVs detected by BoBs and CNV-seq were verified by chromosomal SNP array (SNP Array), and karyotype analysis was used as the gold standard for fetal chromosome number abnormalities. In this study, the two technologies were compared on the accuracy of chromosome number abnormalities, chimeric chromosome number abnormalities, chromosomal microdeletions and micro-duplications, as well as the time required for the main experimental steps, the scope of chromosome abnormality detection, and the detection cost, etc. 

The results showed that a total of 73 chromosomal aneuploidies were detected in 1,876 samples collected. Trisomy 21 accounted for 53.42%, sex chromosome aneuploidy for 24.66%, trisomy 18 for 20.55%, and trisomy 13 for only 1.37%. The detection rate of CNV-seq was 100% (73/73), while the accuracy rate of BoBs detection was 100% on autosomal aneuploidy, but only 83.33% (15/18) on sex chromosome. In terms of CNV detection, a total of 30 pathogenic copy number variations (CNV) were identified in 1,876 samples, accounting for 1.59%. Among them, Xp22.31 microdeletion (ichthyosis) and 22q11 microdeletion (DiGeorge syndrome) had the highest incidence, followed by Williams-Beuren syndrome and Wolf-Hirschhorn syndrome. The remaining pathogenic gene copy number variations included 22q11 duplication, Smith-Magenis syndrome, Prader-Willi syndrome, 1q21.1, 18p11 and Xq11.1 duplication syndromes. Limited by the scope of detection and the types of detection probes, a total of 20 cases (66.67%) of pathogenic CNVs were detected by BoBs detection, 7 cases were abnormal and 3 cases were missed. CNV-seq had good detection performance. A total of 29 cases (96.67%) of pathogenic CNVs were detected, and the remaining 1 case had no detection results due to insufficient sample size. Only 2 cases of pathogenic CNVs with large fragment deletion were found by karyotype analysis. In contrast, in terms of abnormal number of mosaic chromosomes, CNV-seq can detect all abnormalities with chimerism ratio above 10%, but cannot detect abnormalities with chimerism ratio below 10%, while BoBs can only detect abnormalities with chimerism ratio above 50%, and the accuracy of the two technologies is 50% and 30% respectively.

Regarding the cost-effectiveness of the two tests, studies revealed that the testing costs of CNV-seq and BoBs varied in different regions of China, but the price range was between US$350 and US$400. At a similar cost, BoBs test provides the detection of 14 common pathogenic chromosomal variations, while CNV-seq can detect the aneuploidy of 24 chromosomes and the pathogenic CNVs. Therefore, CNV-seq is a relatively cost-effective prenatal diagnosis method. In addition, in terms of detection time, DNA hybridization is the most time-consuming step in BoBs assay, while DNA sequencing is the most time-consuming step in CNV-seq. But in general, the two techniques are relatively time-consuming, 17-18 hours (CNV-seq) and 23-27 hours (BoBs assay) respectively.


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In summary, BoBs detection and CNV-seq sequencing are two highly accurate prenatal diagnosis methods. Several previous studies have recommended strategies for prenatal diagnosis that combine BoBs or CNV-seq with karyotype analysis, but the two methods have never been directly compared. For the first time, a comprehensive study on the detection accuracy of the two methods and other related aspects of clinical application was conducted. It revealed that CNV-seq is a faster, more accurate and more cost-effective detection technology, which, when combined with karyotype analysis, can provide the best cost-effectiveness ratio for pregnant women, thereby further enhancing China's capacity and effectiveness to prevent and control birth defects. 


Annoroad NGS chromosome abnormality (CNV-seq) detection

Annoroad’s NGS chromosome abnormality detection uses next-generation sequencing technology, which can effectively compensate for the low resolution of karyotyping technology and the failure of cell culture in some cases. It also has a series of advantages. The use of high-throughput sequencing technology can process a large number of samples simultaneously; no cell culture is required to reduce the proportion of test failures; with high detection accuracy, chromosomal small fragment changes and chromosomal microdeletions and microduplications can be found; it can make up for the inaccuracy of karyotype analysis in chromosome abnormality diagnosis; moreover, unknown chromosomal abnormalities can be found.

Introduction to clinical diagnosis technology

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Sample type

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