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| Status |
Public on Nov 23, 2017 |
| Title |
De novo and rare inherited copy-number variations in the hemiplegic form of cerebral palsy |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
The Affymetrix CytoScan HD array is a high resolution SNP platform for studying copy number variations in the human genome. It is widely being used in both clinical and research settings for identifying causative variants as well as interrogating the genome for benign variants. We employed this platform to investigate the risk factor CNVs in trios diagnosed with hemiplegic cerebral palsy. We genotyped 101 unrelated probands and their both parents and compared their genotypes to those of 9,611 population controls, in order to identify rare CNVs (<0.1% frequency) of at least 10 kb in size that might contribute to CP. We uncovered de novo CNVs and Decipher Syndromes in probands. We have identified additional potentially risk factor CNVs impacting the coding sequencing of genes involved in brain functions.
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| Overall design |
We employed Affymetrix Chromsome Analysis Suite (ChAS), iPattern, Nexus, and Partek algorithms to call CNVs from the CytoScan HD array data. We defined a stringent set of variants when each variant was called by at least by two algorithms. We defined the ancestry and relatedness of the samples using PLINK.
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| Contributor(s) |
Scherer SW, Zarrei M |
| Citation(s) |
28771244 |
| Submission date |
Apr 29, 2016 |
| Last update date |
Jul 13, 2018 |
| Contact name |
Stephen W Scherer |
| E-mail(s) |
stephen.scherer@sickkids.ca
|
| Organization name |
The Hospital for Sick Children
|
| Department |
Genetics and Genomic Biology
|
| Street address |
686 Bay Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
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| Platforms (1) |
| GPL16131 |
[CytoScanHD_Array] Affymetrix CytoScan HD Array |
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| Samples (292)
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| Relations |
| BioProject |
PRJNA320060 |
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