The Comprehensive Comparison of Bacterial Artificial Chromosomes (BACs)–on-Beads Assay and Copy Number Variation Sequencing in Prenatal Diagnosis of Southern Chinese Women

Abstract

Bacterial artificial chromosomes (BACs)eon-Beads (BoBs) assay and copy number variation sequencing (CNV-seq) are two frequently used methods in today's prenatal diagnosis. Several studies were conducted to investigate the performance of each approach, but they were never compared side by side. In this article, a comprehensive comparison of BoBs and CNV-seq was conducted using 1876 amniotic fluid and umbilical cord blood samples collected from Fujian Maternity and Child Health Hospital between 2015 and 2019. Karyotyping was used as the gold standard for chromosome structure variation, and chromosomal microarray analysis was performed to validate inconsistent results. Overall, 174 cases of confirmed chromosome anomalies were detected, including 73 chromosomal aneuploidies, 10 mosaics, 30 pathogenic CNVs, and 61 other structural anomalies. BoBs and CNV-seq achieved a 100% concordance in all 55 pathogenic euchromosome aneuploidies, but CNV-seq had a higher detection rate in sex chromosome aneuploidy and mosaic identification. For CNV detection, all of the 20 pathogenic CNVs discovered by the BoBs assay also were identified by CNV-seq and 10 additional pathogenic CNVs were observed by CNV-seq. The results of this study showed that CNV-seq was a reliable and more favorable method in terms of detection rate, costs, and disease range. In combination with karyotyping, CNV-seq could improve the efficiency and accuracy of a prenatal diagnosis to alleviate maternal emotional anxiety and deduce birth defects.

Clinical Utility of the Prenatal BACs-on-Beads™ Assay in Invasive Prenatal Diagnosis

“…Consistent with other studies (Tao et al, 2019;Xu et al, 2020), we found that PNBoBs ™ , at least for common aneuploidies, was highly concordant with karyotyping. Some have recommended that a positive RAD result, without karyotyping, can be directly used as a basis for medical decision-making in clinical management (Ogilvie et al, 2005;Comas et al, 2010).…”

“…With the clinical application of PNBoBs, different perspectives have emerged; some have suggested that it can replace traditional karyotyping (Piotrowski et al, 2012), arguing that PNBoBs ™ can detect most clinical cases of pCNV and that it possesses advantages over traditional karyotyping. However, a more recent, alternative view is that PNBoBs ™ should be replaced by genome-wide CNV analytical techniques, such as CNV-seq (Xu et al, 2020), regardless of the indication for prenatal diagnosis. These different views reflect the complexity of and lack of consensus on application criteria for PNBoBs ™ in prenatal diagnosis.…”

“…Several studies have reported the detection rate of the PNBoBs ™ assay in patients with different indications for prenatal diagnosis, but their classification methods differed. Some classified all fetal ultrasound findings as ultrasound anomalies (Fang et al, 2018;Huang et al, 2018;Tao et al, 2019;Wang Y. et al, 2020), while others further divided findings into ultrasound structural malformations (FUSA) and soft-marker abnormalities (FUSMA) according to existing guidelines (Rosenfeld et al, 2014;Grati et al, 2015). We adopted the latter classification method for this study.…”

“…In a recent study comparing the detection performance of genome-wide copy-number analysis to PNBoBs ™ in prenatal diagnosis (Xu et al, 2020), 10 cases of ambiguous results and two cases of sex-chromosome mosaicism were classified as false negatives by PNBoBs ™ . However, comparable types of karyotypes were accurately detected using PNBoBs ™ in our study, which may be due to our improved data interpretation method for the PNBoBs ™ assay (Jiang et al, 2021); If this hypothesis holds, then the rate of diagnostic agreement between CNV-seq and PNBoBs ™ in Xu's study would be 99.8% (1,873/1,876), indicating that the performance of PNBoBs ™ may not be inferior to that of genome-wide copy number analysis, without distinguishing clinical indications.…”

“…However, to date, there is still no consensus on which patients undergoing invasive prenatal diagnosis are appropriate for PNBoBs ™ testing and how to use its results to make clinical decisions. However, with the use of genome-wide copy-number variation detection techniques, including chromosome microarray analysis (CMA) and copy number variation sequencing (CNV-seq) in prenatal diagnosis (Stosic et al, 2018;Wang H. et al, 2020), doubts have been raised regarding the clinical utility of PNBoBs ™ in invasive prenatal diagnosis (Xu et al, 2020). In this article, we present our recommendations on these issues based on our analysis of laboratory findings from one of the largest prenatal diagnosis centers in southeastern China.…”