|
Status |
Public on Jul 12, 2018 |
Title |
Genotyping data for sample 6-0247-03 |
Sample type |
genomic |
|
|
Source name |
genomic DNA extracted from whole blood
|
Organism |
Homo sapiens |
Characteristics |
gender: Female tissue: whole blood diagnosis: pediatric obesity
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted from whole blood.
|
Label |
Standard Illumina protocol
|
Label protocol |
Standard Illumina protocol for Omni2.5M Beadchip
|
|
|
Hybridization protocol |
Standard Illumina protocol for Omni2.5M Beadchip
|
Scan protocol |
Standard Illumina protocol for Omni2.5M 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 2.5M platform we used iPattern, PennCNV, QuantiSNP, and CNVPartition. 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 |
Jul 13, 2017 |
Last update date |
Jul 12, 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 |
GPL18952 |
Series (2) |
GSE101417 |
Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity [Omni2.5M Beadchip] |
GSE101418 |
Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity |
|