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Series GSE23201 Query DataSets for GSE23201
Status Public on Aug 06, 2010
Title Large rare Deletions in Ashkenazi Jewish schizophrenia cases vs controls
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Schizophrenia is a severe psychiatric illness that affects ~1% of the population and has a strong genetic underpinning. Recently, genome wide analysis of copy number variation (CNV) has implicated rare and de novo events as important in schizophrenia. Here we report a genome-wide analysis of 245 schizophrenia cases and 490 controls, all of Ashkenazi Jewish descent. Since many studies have found an excess burden of large, rare deletions in cases, we limited our analysis to deletions over 500 kb in size. We observed seven large, rare deletions in cases with 57% of these being de novo. We focused on one 836 kb de novo deletion at chromosome 3q29 that falls within a 1.3–1.6 Mb deletion previously identified in children with intellectual disability (ID) and autism, as increasing evidence suggests an overlap of specific rare CNVs between autism and schizophrenia. By combining our data with prior CNV studies of schizophrenia and analysis of the data of the Genetic Association Information Network (GAIN), we identified six 3q29 deletions among 7,545 schizophrenic subjects and one among 39,748 controls, resulting in a statistically significant association with schizophrenia (p = 0.02) and an odds ratio estimate of 17 (95% CI: 1.36–1198.4). Moreover, this 3q29 deletion region contains two linkage peaks from prior schizophrenia family studies, and the minimal deletion interval implicates 20 annotated genes, including PAK2 and DLG1, both paralogous to X-linked ID genes and now strong candidates for schizophrenia susceptibility.
Overall design Copy Number alanysis was performed on 245 cases and 490 controls of Ashkenazi Jewish descent. Samples were analyzed for deletions greater than 500 kb, with 20 or more snps in the interval. Three algorithms were used for analysis, GADA, GLAD and BEAST. The reference was created by using all samples processed here as the reference.
Contributor(s) Mulle JG, Warren ST
Citation(s) 20691406
Submission date Jul 27, 2010
Last update date Nov 27, 2018
Contact name Jennifer Gladys Mulle
Phone 404-727-0405
Fax 404-727-3949
Organization name Emory Univeristy School of Medicine
Department Department of Human Genetics
Lab Warren Lab
Street address 615 Michael Street, Room 375, Whitehead Bldg
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (735)
GSM574169 1A1_SZ_case
GSM574170 1A4_SZ_case
GSM574171 1A7_SZ_case
BioProject PRJNA131535

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
GSE23201_RAW.tar 47.1 Gb (http)(custom) TAR (of CEL, TXT)
Processed data provided as supplementary file

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