Chromosome analysis suite 4

We performed chromosome microarray analysis to detect CNVs in the fetuses. Fetal uncultured genomic DNA was extracted using a DNA extraction kit (QIAamp DNA Mini Kit, QIAGEN, Germany). CMA was conducted as in previous literature (Huang et al., 2021 (link); Hu et al., 2022 (link)), which was performed using a whole-genome CytoScan 750K array (Thermo Fisher Scientific, United States). The raw data analyzed with the Chromosome Analysis Suite 4.0 (Thermo Fisher Scientific, United States) were checked and compared carefully with the genome version GRCh37/hg19. According to the deletion and duplication in chromosome location, the clinical significances of chromosomal abnormalities were evaluated and defined as five types of properties, including pathogenicity, likely pathogenicity, benign, likely benign, and variant of uncertain significance.

Fetal uncultured genomic DNA was extracted using a DNA extraction kit (QIAamp DNA Mini Kit, QIAGEN, Germany). CMA was performed using a whole-genome CytoScan 750K array (Thermo Fisher Scientific, USA), as recommended by the manufacturer. The raw data were analyzed with the Chromosome Analysis Suite 4.0 (Thermo Fisher Scientific, USA) based on the genome version GRCh37/hg19. Mosaic trisomy was reported when the median calibrated log2 ratio of a chromosome was between 2.10 (10%) and 2.90 (90%). When a low-level mosaic trisomy (10% to 30%) was found by CMA, karyotyping and an interphase FISH were recommended to further verify, and the NIPS result and clinical manifestation should be taken into account if available.

A microarray analysis was performed on high-density microarrays (DNA chips) of an Affymetrix (USA) CytoScan^TM HD Array to determine the presence of chromosomal aberrations of the BRCA1 gene. Sample preparation, hybridization, and scanning procedures were performed according to the manufacturer’s protocol of an Affymetrix GeneChip^® Scanner 3000 7G system (Affymetrix, Santa Clara, CA, USA). To process the results of microchipping, we used Chromosome Analysis Suite 4.0 (Affymetrix, Santa Clara, CA, USA) for the detection of aberrations—deletions or amplifications (losses or gains)—and loss of heterozygosity (LOH).