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Series GSE31575 Query DataSets for GSE31575
Status Public on Jan 15, 2012
Title Ribosomal Protein Gene Deletions in Diamond Blackfan Anemia
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Genome variation profiling by genome tiling array
Summary Diamond Blackfan anemia is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, often with associated physical abnormalities. Perturbations of the ribosome appear critically important to the development of DBA, as alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins. However, presently only 50-60% of patients have an identifiable genetic lesion by ribosomal protein gene sequencing.
Using genome-wide SNP array to evaluate for regions of recurrent copy variation, we identified deletions at known DBA-related ribosomal protein gene loci in 17% (9/51) of patients without an identifiable mutation, including RPS19, RPS17, RPS26, and RPL35A
 
Overall design [Illumina platforms] A total of 68 samples were analyzed on Illumina Omni1_Quad or Illumina OmniExpress Genotyping bead arrays; 51 affected probands, 1 affected sibling, 1 unaffected sibling, and 15 parents.

[NimbleGen platform] 5 samples where a deletion was identified by SNP array and one sample where no deletion was identified were run on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused arrays for confirmation.
 
Contributor(s) Farrar JE, Vlachos A, Atsidaftos E, Carlson-Donohoe H, Markello TC, Arceci RJ, Ellis SR, Lipton JM, Bodine DM
Citation(s) 22045982
Submission date Aug 22, 2011
Last update date Feb 19, 2014
Contact name Jason Eli Farrar
E-mail(s) jefarrar@uams.edu
Phone 501-603-1224
Organization name University of Arkansas for Medical Sciences
Department Pediatrics/Hematology-Oncology
Street address 1 Children's Way, #512-10
City Little Rock
State/province AR
ZIP/Postal code 72202
Country USA
 
Platforms (3)
GPL8882 Illumina HumanOmni1-Quad BeadChip
GPL13135 HumanOmniExpress BeadChip
GPL14190 Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused Array [100718_HG18_CGH_CCDS]
Samples (74)
GSM783903 PeripheralBlood_DBA_Proband_2302 [Omni1-Quad]
GSM783904 PeripheralBlood_DBA_Proband_412 [Omni1-Quad]
GSM783905 PeripheralBlood_DBA_Proband_1020 [Omni1-Quad]
Relations
BioProject PRJNA145671

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
GSE31575_RAW.tar 225.0 Mb (http)(custom) TAR (of PAIR)
GSE31575_non-normalized_GPL13135.txt.gz 421.3 Mb (ftp)(http) TXT
GSE31575_non-normalized_GPL8882.txt.gz 355.2 Mb (ftp)(http) TXT
Processed data included within Sample table
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