|
| Status |
Public on Feb 17, 2011 |
| Title |
5993_Child (Mapping250K_Nsp) |
| Sample type |
genomic |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 5993
family member: Child
gender: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from blood samples using the Puregene DNA kit
|
| Label |
Biotin
|
| Label protocol |
DNA samples were processed according to the instructions provided in the Affymetrix GeneChip® Mapping 500K Assay Manual
|
| |
|
| Hybridization protocol |
hybridized to GeneChip® Human Mapping 250K Nsp or 250K Sty arrays in an Affymetrix Hybridization Oven 640
|
| Scan protocol |
images were obtained using an Affymetrix GeneChip® Scanner 3000 7G and GeneChip® Operating Software version 1.4
|
| Data processing |
CNVs were detected using the Copy Number Analysis Tool (CNAT) (release cn-1.5.6_v3.2), which incorporates a Bayesian Robust Linear Model with the Mahalanobis distance classifier (BRLMM) algorithm to perform quantile normalization, followed by regression to reduce the PCR bias due to GC content and fragment length
An HMM-based algorithm implemented in CNAT4 was used to estimate copy number for each SNP in the context of its surrounding SNPs. The Gaussian bandwidth was set to 0 Kb and a minimum of 5 probes was required to detect a CNV. The findings were visualized using GeneChip Genotyping Analysis Software (GTYPE) from Affymetrix.
|
| |
|
| Submission date |
Feb 10, 2011 |
| Last update date |
Feb 17, 2011 |
| Contact name |
Tracy Tucker |
| E-mail(s) |
tbtucker@interchange.ubc.ca
|
| Organization name |
University of British Columbia
|
| Street address |
Box 153 4480 Oak Street
|
| City |
Vancouver |
| ZIP/Postal code |
V6H3V4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3718 |
| Series (2) |
| GSE27216 |
Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Mapping250K_Nsp and Mapping250K_Sty) |
| GSE27367 |
Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR |
|
