Integrated CNV-seq, karyotyping and SNP-array analyses for effective prenatal diagnosis of chromosomal mosaicism

Abstract

Background Emerging studies suggest that low‐coverage massively parallel copy number variation sequencing (CNV-seq) more sensitive than chromosomal microarray analysis (CMA) for detecting low-level mosaicism. However, a retrospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted. Methods A total of 72 mosaicism cases identified by karyotyping or CMA were recruited to the study. There were 67 mosaic samples co-analysed by CMA and CNV-seq, comprising 40 with sex chromosome aneuploidy, 22 with autosomal aneuploidy and 5 with large cryptic genomic rearrangements. Results Of the 67 positive mosaic cases, the levels of mosaicism defined by CNV-seq ranged from 6 to 92% compared to the ratio from 3 to 90% by karyotyping and 20% to 72% by CMA. CNV-seq not only identified all 43 chromosomal aneuploidies or large cryptic genomic rearrangements detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. The improved yield of mosaicism detection by CNV-seq was largely due to the ability to detect low level mosaicism below 20%. Conclusion In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant mosaicism with enhanced resolution and increased sensitivity. This study provides strong evidence for applying CNV-seq as an alternative to CMA for detection of aneuploidy and mosaic variants.

Prenatal Diagnosis of Chromosomal Mosaicism in 18,369 Cases of Amniocentesis

“…The bias between karyotyping and uncultured results was distinct in previous reports. [10][11][12][13][14] Most reports involving mosaicisms focused on CPM and true fetal mosaicisms (TFM) in chorionic villus sampling rather than TFM itself in AF. In the present study, we also compared the mosaic ratio of two cultures, and the CV value was as high as 118.5%.…”

Clinical Selection of Prenatal Diagnostic Techniques Following Positive Noninvasive Prenatal Screening Results in Southwest China

“…CNVseq based on massively parallel sequencing has several beneficial features, such as low cost, high throughput, low demand of DNA (10 ng), and high resolution (0.1 Mb). CNVseq has been demonstrated to be a suitable first-tier diagnostic test for the identification of clinically significant fetal chromosome anomalies, and it has shown similar effectiveness and advantages in the clinical diagnosis of aneuploidy and pCNVs (Ma et al, 2021). CNVseq could even detect some CNVs that were omitted by CMA because of insufficient probes within the corresponding regions and showed a higher sensitivity in detecting low-level mosaicism than CMA (Walker et al, 2019;Wang et al, 2020).…”

Application of the prenatal BACs-on-Beads™ assay for rapid prenatal detection of sex chromosome mosaicism

“…With the development of molecular biology, a variety of molecular diagnostic techniques have emerged to be used in clinical. In recent years, SNP-array and CNV-seq had been widely applied to detect chromosome variation in the whole genome, and the detectable levels were 30% to 70% by Affymetrix arrays (Pinto et al 2018 ; Zahir and Marra, 2015 ), and the levels of mosaicism detected by CNV-seq ranged from 6 to 92% (Ma et al 2021 ). In our study, the proportion of sex chromosome mosaicism detected by SNP-array and CNV-seq were 4.8%, especially for sSMC, SNP-array and CNV-seq can clarify its source and segment size, they supplemented the limited resolution of conventional karyotyping.…”