Table 1

Detection of gold standard deletions >100 kb

Gold standard deletionSize (bp)WGS detectionArray detection25
chr3:162,514,471–162,625,647111 176All WGSAll Agilent arrays*
chr4:69,375,591–69,491,543115 952All WGSAffymetrix Cytoscan HD
Affymetrix SNP 6.0
Agilent 2×400K CNV*
Illumina HumanOmni1Quad-v1
Illumina HumanOmni2.5–8 v1
Illumina HumanOmni25Exome-8v1
Illumina HumanOmni5-4v1
Illumina HumanOmni5Exome-v1
chr4:70,122,981–70,231,746108 765All WGSAffymetrix SNP 6.0
Agilent 2×400K CNV*
Illumina HumanOmni1Quad-v1
Illumina HumanOmni2.5–8 v1
Illumina HumanOmni25Exome-8v1
chr6:78,892,808–79,053,430160 622All WGSAffymetrix Cytoscan HD
Affymetrix SNP 6.0
Agilent 2×400K CNV*
Illumina HumanOmni1Quad-v1
Illumina HumanOmni2.5–8 v1
Illumina HumanOmni25Exome-8v1
Illumina HumanOmni5-4v1
Illumina HumanOmni5Exome-v1
Illumina HumanOmniExpressExome 1.2
chr8:39,195,825–39,389,230193 405All WGSAffymetrix Cytoscan HD
Affymetrix SNP 6.0
Agilent 2×400K CNV*
Illumina HumanOmni1Quad-v1
Illumina HumanOmni2.5–8 v1
chr11:4,248,265–4,353,229104 964All WGSAffymetric SNP 6.0
Agilent 2×400K CNV
Agilent 1×1 M HR
chr19:20,595,835–20,717,950122 115All WGSAll arrays except Illumina Psych Array

  • *Called as high copy duplication.

  • WGS, whole-genome sequencing.