DNA samples were processed via SNP array analysis using the Affymetrix GeneChip 250K Nsp or CytoScan HD (Affymetrix, Santa Clara, CA, USA) according to the protocol provided by the manufacturer. Informatics analysis of the SNP array data was conducted using the CNAG/AsCNAR software, which enables the accurate detection of allelic status without paired normal DNA, even in the presence of up to 70–80% normal cell contamination50. Isochromosome 12p was confirmed when a sample had two more copies of 12p than of 12q. To confirm the copy number abnormalities detected using the SNP array, NGS-based copy number analyses were also performed in all samples using the in-house pipeline, CNACS51, which enable digital karyotyping.
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