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Status |
Public on Jun 30, 2011 |
Title |
NA18517 rep 3 genotyping at TCAG (Human660W-Quad) rev2 |
Sample type |
genomic |
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Source name |
NA18517
|
Organism |
Homo sapiens |
Characteristics |
gender: Female cell type: lymphoblastoid cell lines cell line: GM18517 genotyping center: TCAG
|
Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18517
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
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Label |
C-Bio and A-DNP
|
Label protocol |
Standard Illumina protocol for Human660W-Quad Beadchip
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|
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Hybridization protocol |
Standard Illumina protocol for Human660W-Quad Beadchip
|
Scan protocol |
Standard Illumina protocol for Human660W-Quad Beadchip
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Description |
Genomic DNA extracted was analyzed using Illumina's BeadStudio software
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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 1M platform we used QuantiSNP, iPattern, PennCNV, cnvPartition and Partek 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 |
Mar 22, 2011 |
Last update date |
Jun 30, 2011 |
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 |
GPL8888 |
Series (2) |
GSE25893 |
A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants |
GSE28103 |
A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Human660W-Quad) |
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