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| 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
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| 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.
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| 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.
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| Contributor(s) |
Mulle JG, Warren ST |
| Citation(s) |
20691406 |
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| Submission date |
Jul 27, 2010 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Jennifer Gladys Mulle |
| E-mail(s) |
jmulle@emory.edu
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| Phone |
404-727-0405
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| Fax |
404-727-3949
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| Organization name |
Emory Univeristy School of Medicine
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| Department |
Department of Human Genetics
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| Lab |
Warren Lab
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| Street address |
615 Michael Street, Room 375, Whitehead Bldg
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (735)
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| Relations |
| BioProject |
PRJNA131535 |
| 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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