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Series GSE27251 Query DataSets for GSE27251
Status Public on Feb 17, 2011
Title Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (NimbleGen)
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. We determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP array. The Affymetrix 500K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosome CNVs in 30 trios. 147 of these CNVs were de novo, but only 33 (22%) of the de novo CNVs were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 pathogenic and 4 possibly pathogenic CNVs for MR. All 11 of these CNVs were detected by both the Agilent and NimbleGen arrays, 9 by the Affymetrix 500K and Illumina beadchips, and 5 by the SMRT BAC array. Two of the 4 pathogenic or possibly pathogenic CNVs present in the trios tested with the Affymetrix 6.0 array were identified. Our findings demonstrate that different results are obtained with different AGH platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls supports the need for validating clinically important findings with a different methodology.
Overall design 30 trios were analysed consisting of child (proband) and both normal parents.
Contributor(s) Tucker T, Montpetit A, Chai D, Chan S, Chénier S, Coe BP, Delaney A, Eydoux P, Lam WL, Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Lmichaud J, Friedman JM
Citation(s) 21439053
Submission date Feb 11, 2011
Last update date Sep 19, 2012
Contact name Tracy Tucker
Organization name University of British Columbia
Street address Box 153 4480 Oak Street
City Vancouver
ZIP/Postal code V6H3V4
Country Canada
Platforms (1)
GPL7717 WiCell HG18 WG CGH 385K v2
Samples (60)
GSM673709 1056_Child_Father (NimbleGen)
GSM673710 1056_Child_Mother (NimbleGen)
GSM673711 1511_Child_Father (NimbleGen)
This SubSeries is part of SuperSeries:
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR
BioProject PRJNA141823

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE27251_RAW.tar 1.4 Gb (http)(custom) TAR (of PAIR, TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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