Total genomic DNA was isolated by using QIAamp® DNA Blood Mini Kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol.
Label
Biotin
Label protocol
As per manufacturer (Affymetrix)
Hybridization protocol
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Data processing
The array image was acquired using Chromosome Analysis Suite software (Affymetrix GeneChip Convert Console, Santa Clara, USA) and Chromosome Analysis Suite Version 2.0.0.. Log2 ratio and B Allele Frequency (BAF) values were plotted along chromosomal coordinates, allowing the detection of both copy number changes and copy neutral regions of homozygosity (ROH). The size threshold for CNVs analysis was set at > 50 kb for gains, > 25 kb for losses, and > 10 Mb for loss of heterozygosity. Data interpretation followed the ACMG guideline.
