Genome-wide CNV Detection by Sequencing

Single end sequencing was performed on the NextSeq CN500 platform (Illumina, San Diego, CA, USA) with a run time of 6.5 h to generate approximately 5 million raw 45 bp reads per sample. Raw reads were then edited to remove artificial adaptor sequences, and the true 36 bp genome sequences were then mapped to the hg19 reference genome using the Burrows and Wheeler algorithm [18 (link)]. On average, approximately 2.8–3.2 million reads were uniquely mapped for data analysis. Reads were allocated to 20 kb bins along the length of each chromosome, and CNVs were identified from 24 chromosome copy number (CN) plots, as previously described [13 (link),19 (link)]. Duplications were defined as CN >2.8, deletions CN <1.2, disomy (1.8 < CN < 2.2), mosaic trisomy (2.2 < CN < 2.8) and mosaic monosomy (1.2 < CN < 1.8).
Genomic variant databases including DGV (Database of Genomic Variants), http://projects.tcag.ca/variation), OMIM (Online Mendelian Inheritance in Man) (http://www.omim.org), PubMed (http://www.ncbi.nlm.nih.gov/pubmed) and UCSC (University of California, Santa Cruz) (http://genome.ucsc.edu/, hg19) were used as a reference source of CNVs. The pathogenicity of detected CNVs was assessed following ACMG guidelines [20 (link)].