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.