Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Custom array CGH validation of de novo CNVs in asthma samples

ABSTRACT: This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent. We attempted to validate 9 de novo CNVs in the same number of trios. In 3 cases, paternal DNA was not available leaving a total of 24 distinct samples for hybridization. All samples were hybridized against a previously well-characterized reference (NA15510; see Tuzun et al., Nat Genet 2005).

ORGANISM(S): Homo sapiens

SUBMITTER: Andy Itsara

PROVIDER: E-GEOD-23572 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Custom array CGH validation of de novo CNVs in asthma samples

Project description:This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent.

2010-09-01 | GSE23572 | GEO

Custom array CGH validation of de novo CNVs in CEU HapMap samples

Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459. 12 samples were hybridized in each of the three pedigrees (36 samples total) against a previously well-characterized reference (GM15510; see Tuzun et al., Nat Genet 2005).

2010-09-01 | E-GEOD-23575 | biostudies-arrayexpress

CGH validation of de novo CNVs in asthma and CEU HapMap samples

Project description:This SuperSeries is composed of the following subset Series: GSE23572: Custom array CGH validation of de novo CNVs in asthma samples GSE23575: Custom array CGH validation of de novo CNVs in CEU HapMap samples Refer to individual Series

2010-09-01 | E-GEOD-23645 | biostudies-arrayexpress

Individuals with excess numbers of germline de novo CNVs [Agilent]

Project description:We describe a multiple de novo CNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional de novo CNVs. Five such families are studied, which consists of four trios and one singleton. Various array platforms are used to interogate these families to identify de novo CNVs.

2016-10-14 | GSE87913 | GEO

Individuals with excess numbers of germline de novo CNVs [NimbleGen]

2016-10-14 | GSE87909 | GEO

Individuals with excess numbers of germline de novo CNVs [Illumina]

2016-10-14 | GSE87838 | GEO

Individuals with excess numbers of germline de novo CNVs [Affymetrix]

2016-10-14 | GSE87802 | GEO

Custom array CGH validation of de novo CNVs in CEU HapMap samples

2010-09-01 | GSE23575 | GEO

Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (NimbleGen)

Project description: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. 30 trios were analysed consisting of child (proband) and both normal parents.

2011-02-17 | E-GEOD-27251 | biostudies-arrayexpress

Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Agilent 244K)

2011-02-17 | E-GEOD-27229 | biostudies-arrayexpress