2.4 | CMA and LD-WGS
CMA was performed using an Illumina HumanCytoSNP-12 platform (Illumina, San Diego, CA, USA). The array employs both Copy Number Changes (CNC) and Single Nucleotide Polymorphism (SNP) probes on a whole genome array with a 30 Kb resolution. A higher resolution was used for all regions known to be associated with balanced and unbalanced structural variants. The data were analyzed in Illumina KaryoStudio version 1.4.3.0 (Illumina, San Diego, CA, USA) and reported using NCBI human genome build 37.1 (hg19) following ISCN nomenclature.
The LD-WGS-based CNV analysis was performed by GC Genome (Yongin, Korea). Briefly, genomic DNA was extracted from peripheral-blood leukocytes, sheared to a target size of 250 bp, and sequenced on a NextSeq 500 platform (Illumina, CA, USA) in 75 bp single-read mode. CNV calling for 3.1 million sequence reads was performed using DNAcopy software v1.38. Using the target-specific reference mapping ratio values for the target sample and the normal controls, we calculated the copy number status of each targeted sample. The February 2009 Human reference sequence (GRCh37/hg19) was used for genome assembly.