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Sample GSM672419 Query DataSets for GSM672419
Status Public on Feb 17, 2011
Title 4821_Child (Mapping250_Nsp)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 4821
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

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 NC 0.636920 AA 0.331674 11.836456
AFFX-2315061 AA 0.095351 AA 0.705500 10.798893
AFFX-2315062 AB 0.375869 AB 0.159858 10.524112
AFFX-2315057 AB 0.085740 AB 0.020680 10.964387
AFFX-2315058 AA 0.494666 AA 0.576580 10.920699
AFFX-2315059 AB 0.056455 AB 0.376685 10.739786
AFFX-2315063 AA 0.100281 AA 0.648995 10.665713
AFFX-2315064 BB 0.129855 BB -0.425924 10.543245
AFFX-2315065 BB 0.402627 BB -0.343609 10.204595
AFFX-2315066 NC 0.633112 BB -0.410957 10.792346
AFFX-2315067 NC 0.550971 AB 0.266876 11.520242
AFFX-2315068 AB 0.006507 AB 0.164896 10.747184
AFFX-2315069 AB 0.149657 AB -0.293939 10.274302
AFFX-2315070 BB 0.044406 BB -0.607965 10.724330
AFFX-2315071 AB 0.011559 AB -0.181859 9.758270
AFFX-2315072 AA 0.367875 AA 0.398401 11.246452
AFFX-2315073 NC 0.781110 AA 0.534588 11.169735
AFFX-2315074 BB 0.090914 BB -0.498859 10.427910
AFFX-2315075 AB 0.054520 AB 0.169899 12.048095
AFFX-2315076 AB 0.276646 AB 0.205546 11.061452

Total number of rows: 262314

Table truncated, full table size 12358 Kbytes.




Supplementary file Size Download File type/resource
GSM672419_4821_Child_Nsp.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM672419_4821_Child_Nsp.chp.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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