|
| Status |
Public on Jun 30, 2011 |
| Title |
NA18980 rep1 genotyping at HMS (Human660W-Quad) rev2 |
| Sample type |
genomic |
| |
|
| Source name |
NA18980
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
cell type: lymphoblastoid cell lines
cell line: GM18980
genotyping center: HMS
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18980
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Standard Illumina protocol for Human660W-Quad Beadchip
|
| |
|
| Hybridization protocol |
Standard Illumina protocol for Human660W-Quad Beadchip
|
| Scan protocol |
Standard Illumina protocol for Human660W-Quad Beadchip
|
| Description |
Genomic DNA extracted was analyzed using Illumina's BeadStudio software
|
| 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.
|
| |
|
| 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) |
|
