Karyostudio v1

Genomic DNA were extracted using QIA amp DNA Mini Kit (Qiagen). In our center, tissue samples, such as placental tissues and fetal tissues, were tested using the platform of Human cyto12 SNP array, whereas other samples, such as peripheral blood samples and amniotic fluid cells, were tested using the platform of CytoScan 750K array. For Illumina array platform, Human cyto12 SNP array (Illumina) comprising approximately 300,000 SNP probes was applied for the whole‐genome scan. Molecular karyotype analysis was performed by KaryoStudio V 1.4.3.0 (Illumina). For Affymetrix array platform, CytoScan 750K array (Affymetrix) comprising approximately 550,000 copy number CNVs probes and 200,000 SNP probes were applied for the whole‐genome scan. Molecular karyotype analysis was performed by Affymetrix Chromosome Analysis Suite (ChAS). CNVs of two array platforms were all called at an effective minimal resolution of 100kb involving at least 10 contiguous probes.

Analysis was performed for all samples on chromosomes 21, 18, 13, SCAs, RATs, and CNVs. Pregnant women with positive NIPT results were advised to undergo amniocentesis. Prenatal diagnosis methods included karyotyping and/or chromosomal microarray analysis (CMA).
Amniotic fluid cell culture was performed according to the standard techniques. Routine G-bands by trypsin using Giemsa (GTG) analysis at 400-band resolution was used to prepare the amniotic cell chromosome specimens (Zheng et al., 2019 (link)).
Human cyto12 SNP array (Illumina, United States) comprising around 300,000 SNP probes was applied for whole-genome scan on the amniotic cell DNA of the fetus. SNP-array tests were performed according to the manufacturer’s protocol (Illumina, United States); molecular karyotype analysis was carried out by KaryoStudio V 1.4.3.0 (Illumina, United States). Databases such as DECIPHER¹, DGV², UCSC³, and OMIM⁴ were used as references to evaluate the array data and analyze genotype–phenotype correlations (Zheng et al., 2019 (link)).
Three months after the diagnosis, these pregnant women were followed up for pregnancy outcomes. Pregnant women with negative NIPT results were recommended to continue routine prenatal examinations. These cases were interviewed by telephone 3 months after delivery to obtain information on neonatal outcome.

The HumanCytoSNP-12 DNA Analysis Bead Chip (Illumina, Inc., San Diego, CA, USA) was used for SNP-array analysis according to the manufacturer’s protocol and molecular karyotype analysis was performed using KaryoStudio V 1.4.3.0 (Illumina, Inc., San Diego, CA, USA). A range of chromosomal abnormalities were included: (1) autosomal and sex chromosome aneuploidy; (2) mosaicism for autosomal and sex chromosome aneuploidy greater than 30%; (3) deletion of CNVs on chromosomes greater than 1 mega base pair (Mb); (4) CNV duplications on chromosomes greater than 2 Mb; (5) loss of heterozygosity greater than 5 Mb; (6) mosaicism for deletion, duplication of CNVs ≥ 5 Mb greater than 30%.