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Sample GSM696197 Query DataSets for GSM696197
Status Public on Jun 30, 2011
Title NA18517 rep1 genotyping at TCAG (Illumina_650Y) rev2
Sample type genomic
 
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.
Label C-Bio and A-DNP
Label protocol Standard Illumina protocol for Illumina_650Y Beadchip
 
Hybridization protocol Standard Illumina protocol for Illumina_650Y Beadchip
Scan protocol Standard Illumina protocol for Illumina_650Y 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 GPL6987
Series (2)
GSE25893 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants
GSE28102 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Illumina_650Y)

Data table header descriptions
ID_REF
Allele1
Allele2
GC Score
Theta
R
B Allele Freq
VALUE Log R Ratio

Data table
ID_REF Allele1 Allele2 GC Score Theta R B Allele Freq VALUE
MitoA10045G-13273284_B_R_IFB1141652022:0 A A 0.3197 0.008 3.745 0.0028 -0.2858
MitoA10551G-13273286_T_F_IFB1141639111:0 A A 0.2985 0.030 4.478 0.0067 -0.3224
MitoA11252G-13273288_B_R_IFB1141661584:0 A A 0.3292 0.024 4.856 0.0061 -0.2492
MitoA11468G-13273289_B_R_IFB1141719645:0 A A 0.3187 0.020 5.254 0.0031 -0.2551
MitoA11813G-13273292_T_F_IFB1141667833:0 A A 0.2514 0.066 4.221 0.0254 -0.3008
MitoA12309G-13273294_T_F_IFB1141664161:0 A A 0.2885 0.031 4.003 0.0100 -0.3063
MitoA13106G-13273298_B_R_IFB1141641623:0 A A 0.3484 0.044 1.290 0.0240 -0.2814
MitoA13264G-13273299_T_F_IFB1141660858:0 A A 0.2567 0.032 5.594 0.0044 -0.2673
MitoA13781G-13273301_T_F_IFB1141687043:0 A A 0.3457 0.050 1.290 0.0015 0.0175
MitoA14234G-13273304_T_F_IFB1141674277:0 A A 0.3183 0.020 2.513 0.0027 -0.3970
MitoA14583G-13273306_T_F_IFB1141688843:0 A A 0.3297 0.016 1.848 0.0039 -0.2952
MitoA15219G-13273311_T_F_IFB1141717824:0 - - 0.0000 0.257 0.378 0.2399 -3.7715
MitoA15245G-13273312_B_R_IFB1141677374:0 A A 0.3195 0.063 2.988 0.0259 0.1467
MitoA15302G-13273313_T_F_IFB1141686491:0 A A 0.2736 0.038 5.671 0.0122 -0.3259
MitoA15759G-13273316_B_R_IFB1141715135:0 A A 0.3470 0.017 5.174 0.0060 -0.2952
MitoA15925G-13273318_T_F_IFB1141694300:0 A A 0.2904 0.033 2.728 0.0016 -0.5305
MitoA16163G-13273319_T_F_IFB1141711520:0 A A 0.2528 0.072 5.459 0.0297 -0.2317
MitoA16164G-13273320_T_F_IFB1141715312:0 A A 0.3183 0.023 3.334 0.0070 -0.4307
MitoA1738G-13273322_T_F_IFB1141639534:0 A A 0.3015 0.026 4.859 0.0069 -0.3335
MitoA3349G-13273328_T_F_IFB1141711832:0 A A 0.2904 0.048 5.831 0.0199 -0.2726

Total number of rows: 660918

Table truncated, full table size 46247 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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