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| Status |
Public on Feb 17, 2011 |
| Title |
Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Illumina HumanHap550) |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| 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.
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| Overall design |
30 childern with MR
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| 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 |
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| Submission date |
Feb 16, 2011 |
| Last update date |
Sep 19, 2012 |
| Contact name |
Tracy Tucker |
| E-mail(s) |
[email protected]
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| Organization name |
University of British Columbia
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| Street address |
Box 153 4480 Oak Street
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| City |
Vancouver |
| ZIP/Postal code |
V6H3V4 |
| Country |
Canada |
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| Platforms (1) |
| GPL6433 |
Illumina HumanHap550 Genotyping BeadChip v1 |
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| Samples (30)
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| This SubSeries is part of SuperSeries: |
| GSE27367 |
Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR |
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| Relations |
| BioProject |
PRJNA141851 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE27364_Matrix_Processed.txt.gz |
288.3 Mb |
(ftp)(http) |
TXT |
| GSE27364_Matrix_Signal.txt.gz |
216.2 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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