Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation

BMC Med Genomics. 2011 Mar 25;4:25. doi: 10.1186/1755-8794-4-25.

Abstract

Background: Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their comparative performance in a clinical context.

Methods: We studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500 K GeneChip SNP arrays, Agilent Human Genome 244 K oligonucleotide arrays and NimbleGen 385 K Whole-Genome oligonucleotide arrays. We also determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32 K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP arrays.

Results: The Affymetrix 500 K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosomal CNVs in the 30 trios. 147 of these CNVs appeared to be de novo, but only 34 (22%) were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 most likely pathogenic and 2 possibly pathogenic CNVs for MR. All 9 of these putatively pathogenic CNVs were detected by the Affymetrix 500 K, Agilent, NimbleGen and the Illumina arrays, and 5 were found by the SMRT BAC array. Both putatively pathogenic CNVs identified in the 15 trios tested with the Affymetrix 6.0 were identified by this platform.

Conclusions: Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Child
  • Chromosomes, Human, X
  • Comparative Genomic Hybridization / methods*
  • Gene Dosage / genetics*
  • Genetic Association Studies
  • Genotype
  • Humans
  • Intellectual Disability / genetics*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Reagent Kits, Diagnostic

Substances

  • Reagent Kits, Diagnostic

Associated data

  • GEO/GSE27367