Transcriptomics

Dataset Information

5

Transcription profiling of human children with mental retardation and immediate family members


ABSTRACT: 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. Experiment 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. Experiment Overall Design: 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.

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Homo sapiens  

DISEASE(S): Normal,Mentally Retarded

SUBMITTER: BCGSC BC Cancer Agency  

PROVIDER: E-GEOD-7226 | ArrayExpress | 2008-06-21

SECONDARY ACCESSION(S): GSE7226PRJNA98281

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation.

Friedman J M JM   Baross Agnes A   Delaney Allen D AD   Ally Adrian A   Arbour Laura L   Armstrong Linlea L   Asano Jennifer J   Bailey Dione K DK   Barber Sarah S   Birch Patricia P   Brown-John Mabel M   Cao Manqiu M   Chan Susanna S   Charest David L DL   Farnoud Noushin N   Fernandes Nicole N   Flibotte Stephane S   Go Anne A   Gibson William T WT   Holt Robert A RA   Jones Steven J M SJ   Kennedy Giulia C GC   Krzywinski Martin M   Langlois Sylvie S   Li Haiyan I HI   McGillivray Barbara C BC   Nayar Tarun T   Pugh Trevor J TJ   Rajcan-Separovic Evica E   Schein Jacqueline E JE   Schnerch Angelique A   Siddiqui Asim A   Van Allen Margot I MI   Wilson Gary G   Yong Siu-Li SL   Zahir Farah F   Eydoux Patrice P   Marra Marco A MA  

American journal of human genetics 20060725 3


The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically detectable chromosomal abnormalities are the most frequently 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 studie  ...[more]

Similar Datasets

2011-02-17 | E-GEOD-27145 | ArrayExpress
2011-02-17 | E-GEOD-27216 | ArrayExpress
2007-06-23 | GSE7391 | GEO
| GSE27216 | GEO
2011-02-17 | E-GEOD-27251 | ArrayExpress
2011-02-17 | E-GEOD-27229 | ArrayExpress
2010-05-01 | GSE20533 | GEO
| GSE13117 | GEO
2016-01-01 | S-EPMC4891738 | BioStudies
| GSE27364 | GEO