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Sample GSM694403 Query DataSets for GSM694403
Status Public on Jun 30, 2011
Title NA18576 rep1 at TCAG (Human1Mv1_C)
Sample type genomic
 
Source name NA18576
Organism Homo sapiens
Characteristics cell line: GM18576
genotyping center: TCAG
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18576
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 Infinium 1M-single Beadchip
 
Hybridization protocol Standard Illumina protocol for Infinium 1M-single Beadchip
Scan protocol Standard Illumina protocol for Infinium 1M-single 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 GPL6983
Series (2)
GSE25893 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants
GSE28092 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Human1Mv1_C)

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
rs758676-126_B_F_IFB1136519662:0 G G 0.8100 0.987 0.931 1.0000 0.0713
rs3916934-123_B_F_IFB1136503411:0 G G 0.9114 0.996 0.860 1.0000 -0.0090
rs2711935-126_T_R_IFB1138365211:0 A G 0.9032 0.609 1.477 0.5395 -0.0573
rs17126880-123_T_R_IFB1140054009:0 A A 0.9278 0.038 1.289 0.0114 0.1104
rs12831433-126_B_F_IFB1138385824:0 A A 0.8485 0.029 2.175 0.0054 0.0191
rs12797197-126_B_F_IFB1138411445:0 A A 0.8584 0.067 0.381 0.0153 0.1155
rs11002902-126_B_R_IFB1138389502:0 G G 0.7966 0.994 1.489 1.0000 -0.1919
rs3924674-126_T_R_IFB1136512840:0 G G 0.8702 0.995 0.491 1.0000 -0.1511
rs2147587-126_T_F_IFB1154866225:0 A G 0.9660 0.542 1.096 0.4965 -0.1016
rs11983370-126_T_R_IFB1140050766:0 A A 0.7943 0.023 2.421 0.0067 0.0424
rs7167305-126_T_R_IFB1138332395:0 C C 0.8901 0.999 1.072 1.0000 -0.2252
rs715350-126_B_R_IFB1136460923:0 A A 0.9414 0.031 1.290 0.0072 0.1412
rs2635442-126_T_R_IFB1136432512:0 G G 0.8315 0.995 0.832 1.0000 -0.0331
rs7055953-123_T_R_IFB1138374757:0 A G 0.7232 0.700 0.787 0.5801 0.0150
rs7979673-116_B_F_IFB1138390720:0 G G 0.9358 0.991 1.116 1.0000 -0.0470
rs6424572-126_B_F_IFB1136436775:0 A A 0.9519 0.007 0.486 0.0017 -0.2864
rs10829026-120_B_F_IFB1136494680:0 G G 0.8892 0.995 0.311 1.0000 0.2296
rs7037313-126_B_F_IFB1136521486:0 A G 0.8814 0.662 1.053 0.5064 0.4330
rs5920594-114_B_F_IFB1138334897:0 A A 0.8078 0.007 0.904 0.0029 0.0448
rs16972915-123_B_F_IFB1138342491:0 A G 0.9465 0.619 1.353 0.5168 -0.0670

Total number of rows: 1072820

Table truncated, full table size 75226 Kbytes.




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

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