|
| Status |
Public on Nov 21, 2018 |
| Title |
204526 (control) |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from Saliva Samples
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
status: control
tissue: saliva
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was obtained from saliva collection kits, and extracted using manufactures protocols.
|
| Label |
Standard Illumina protocol
|
| Label protocol |
Standard Illumina protocol for Illumina HumanOmni 2.5M chip
|
| |
|
| Hybridization protocol |
Standard Illumina protocol for Illumina HumanOmni 2.5M chip
|
| Scan protocol |
Standard Illumina protocol for Illumina HumanOmni 2.5M chip
|
| Description |
Copy number variation in fetal alcohol spectrum disorder
|
| Data processing |
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina platform we used iPattern, PennCNV, and QuantiSNP. We defined a stringent set of variants when each variant was called by at least by two algorithms.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.
|
| |
|
| Submission date |
Aug 14, 2017 |
| Last update date |
Nov 21, 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 |
| |
|
| Platform ID |
GPL23136 |
| Series (1) |
| GSE102650 |
Copy number variation in fetal alcohol spectrum disorder |
|
