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Series GSE7226 Query DataSets for GSE7226
Status Public on Mar 12, 2007
Title Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation.
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically-detectable chromosomal abnormalities are the most frequent recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy number variants. We studied 100 children with idiopathic mental retardation and their parents using the Affymetrix GeneChip® Mapping 100K Assay and found de novo duplications as small as 1.1 Mb in three cases, de novo deletions as small as 178 kb in eight cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy number variants as conventional cytogenetic analysis in people with mental retardation.
Keywords: mental retardation, trio analysis, copy number variant, CNV, chromosome aberration, array CGH
Overall design Using the Affymetrix GeneChip® Mapping 100K Assay we studied 100 trios that each included one child with idiopathic mental retardation (MR) and both of his/her unaffected biological parents. We also tested 10 unaffected siblings of the MR children from 10 of the above families. In addition, we analyzed 7 trios (child and both unaffected biological parents) as positive controls with previously identified chromosomal aberrations.
Within each sample ID the four digit number refers to a family. Following this four digit family number, 'c' indicates child with MR, 'm' means unaffected mother, 'f' means unaffected father and 's' means unaffected sibling.
Contributor(s) Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJ, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Varhol R, Van Allen MI, Wilson G, Wong T, Yong S, Zahir F, Eydoux P, Marra MA
Citation(s) 16909388
Submission date Mar 08, 2007
Last update date Dec 22, 2017
Contact name BCGSC BC Cancer Agency
Organization name Canada's Michael Smith Genome Sciences Centre
Department Gene Expression
Lab Marco Marra
Street address 675 West 10th Avenue
City Vancouver
State/province BC
ZIP/Postal code V5Z 1L3
Country Canada
Platforms (2)
GPL2004 [Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array
GPL2005 [Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array
Samples (628)
GSM173736 0064c_hd
GSM173737 0064f_hd
GSM173738 0064m_hd
BioProject PRJNA98281

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
GSE7226_RAW.tar 8.0 Gb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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