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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-12

AUTHORS

Tracy Tucker, Alexandre Montpetit, David Chai, Susanna Chan, Sébastien Chénier, Bradley P Coe, Allen Delaney, Patrice Eydoux, Wan L Lam, Sylvie Langlois, Emmanuelle Lemyre, Marco Marra, Hong Qian, Guy A Rouleau, David Vincent, Jacques L Michaud, Jan M Friedman

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. More... »

PAGES

25

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1755-8794-4-25

DOI

http://dx.doi.org/10.1186/1755-8794-4-25

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1007328686

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21439053


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