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Status |
Public on Nov 21, 2018 |
Title |
204529 (control) |
Sample type |
genomic |
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|
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.
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|
|
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 |
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