Table 1 Features and experimental details of CNV detection platforms used in this study
Array | Total Features | Probe Spacing | Data Source | Platform-Specific Analysis Software | Number of Autosomal CNVs Called (replicate 1, replicate 2) | |
|---|---|---|---|---|---|---|
Platform Specific Analysis | Nexus Analysis | |||||
Affymetrix Arrays | ||||||
Affymetrix CytoScan HD | 2,600,000 Copy Number + 750,000 SNP | 0.88 kb mean probe spacing in RefSeq genes | Affymetrix | Affymetrix Chromosome Analysis Suite | 201,241 | 82,93 |
Affymetrix Genome-Wide Human SNP Array 6.0 | 946,000 Copy Number + 906,000 SNP | 0.7 kb mean probe spacing | Affymetrix & Mc Carroll et al. | Birdsuitea | 151a | 105,112 |
Agilent Arrays | ||||||
Agilent SurePrint G3 Human CGH Microarray, 1×1M (Design ID 021529) | 963,029 (60mers) | 2.1 kb overall median probe spacing (1.8 kb in Refseq genes) | Service Provider | Agilent Genomics Workbench 7.0 | 124,133 | 65,53 |
Agilent SurePrint G3 Human High Resolution Microarray, 1×1M (Design ID 023642) | 963,331 (60mers) | 2.6 kb overall median probe spacing, 3 kb average probe spacing | Service Provider | Agilent Genomics Workbench 7.0 | 155,152 | 177,171 |
Agilent SurePrint G3 Human CGH Microarray, 2×400K (Design ID 021850) | 411,056 (60mers) | 5.3 kb overall median probe spacing (4.6 kb in Refseq genes) | Service Provider | Agilent Genomics Workbench 7.0 | 58,61 | 50,48 |
Agilent SurePrint G3 Human CNV Microarray, 2×400K (Design ID 021365) | 442,892 (60mers) | 1 kb overall median probe spatial resolution in CNVs | Service Provider | Agilent Genomics Workbench 7.0 | 365,365 | 433,489 |
Agilent SurePrint G3 Human CGH Microarray, 4×180K (Design ID 022060) | 170,334 (60mers) | 13 kb overall median probe spacing (11 kb in Refseq genes) | Service Provider | Agilent Genomics Workbench 7.0 | 24,25 | 30,32 |
Illumina Arrays | ||||||
Illumina HumanOmni5Exome v1 | 4,641,128 | 0.63 kb mean, 0.32 kb median probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 426,397 | 66,62 |
Illumina HumanOmni5-4v1 | 4,301,331 | 0.68 kb mean, 0.36 kb median probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 63,61 | 56,61 |
Illumina HumanOmni25Exome-8v1 | 2,583,651 | 1.13 kb mean, 0.57 kb median probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 58,57 | 33,35 |
Illumina HumanOmni25-8v1-1 | 2,338,671 | 1.25 kb mean, 0.66 kb median probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 31,34 | 28,24 |
Illumina HumanOmni1Quad-v1b | 1,134,514 | 1.2 kb mean probe spacing | Service Provider | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 245,263 | 139,143 |
Illumina HumanOmniExpressExome 1.2 | 964,193 | 3.0 kb mean, 1.4 kb median probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 31,34 | 17,17 |
Illumina HumanOmniExpress-24v1-0 | 730,525 | 4.1 kb mean, 2.2 kb median probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 15,12 | 11,10 |
Illumina HumanCoreExome v1.1 | 547,644 | 5.3 kb mean, 1.9 kb median probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 5,4 | 7,6 |
Illumina CytoSNP-850 K | 850,000 (50mers) | 50 kb mean probe spacing, 10–20 kb in 3,262 cytogenetically relevant genes | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 12,17 | 25,21 |
Illumina PsychArray | 571,054 | 5.5 kb mean probe spacing | Illumina | Illumina GenomeStudio 2011.1 and cnvPartition 3.2.0 | 5,4 | 10,9 |