Chromosome analysis suite version 2

Affymetrix CytoScan 750K array platforms were used to detect copy number variants. Genomic DNA extraction was performed using Genomic DNA Extraction kit (QIAamp DNA Blood Mini Kit, QIAGEN GmBH, Hilden, Germany) according to the in-house protocols. The standard experimental procedure incorporated the following steps: digestion, ligation, polymerase chain reaction (PCR), PCR purification, fragmentation, labeling, hybridization, washing, staining and scanning. Data was analyzed using the Chromosome analysis software (Chromosome Analysis Suite version 2.1) (Affymetrix; Thermo Fisher Scientific, Inc.). Copy number variation sequencing (CNV-seq) was performed as previously described [11 (link), 12 (link)].
The conventional genomic and phenotype public databases such as UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/hgGateway), ClinGene (http://www.clinicalgenome.org/), OMIM (http://omim.org), DECIPHER (https://decipher.sanger.ac.uk), DGV (http://dgv.tcag.ca/dgv/app/home) and PubMed (http://www.ncbi.nlm.nih.gov/pubmed) were used for retrieval and interpretation.

CytoScan 750K (Affymetrix, USA) microarray was used to test for copy number variations (CNV), loss of homozygosity (LOH), uniparental disomy (UPD), and mosaicism, according to the manufacturer's instructions. The Affymetrix Gene Chip Command Console software (version 4.0) and Chromosome Analysis Suite (version 2.1) (Affymetrix, USA) were used to analyze the raw data.