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Sample GSM694405 Query DataSets for GSM694405
Status Public on Jun 30, 2011
Title NA18576 rep3 at TCAG (Human1Mv1_C)
Sample type genomic
 
Source name NA15510
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=NA15510
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 0.969 0.924 0.9895 0.0558
rs3916934-123_B_F_IFB1136503411:0 G G 0.9114 0.979 0.655 0.9889 -0.4030
rs2711935-126_T_R_IFB1138365211:0 A G 0.9032 0.554 1.416 0.4796 -0.1320
rs17126880-123_T_R_IFB1140054009:0 A A 0.9278 0.043 1.236 0.0157 0.0482
rs12831433-126_B_F_IFB1138385824:0 A A 0.8485 0.033 2.294 0.0098 0.0956
rs12797197-126_B_F_IFB1138411445:0 A A 0.8584 0.069 0.288 0.0166 -0.2858
rs11002902-126_B_R_IFB1138389502:0 G G 0.7966 0.985 2.031 0.9967 0.2393
rs3924674-126_T_R_IFB1136512840:0 G G 0.8702 0.983 0.409 1.0000 -0.4074
rs2147587-126_T_F_IFB1154866225:0 A G 0.9587 0.586 0.716 0.5446 -0.7000
rs11983370-126_T_R_IFB1140050766:0 A A 0.7943 0.028 2.930 0.0118 0.3179
rs7167305-126_T_R_IFB1138332395:0 C C 0.8901 0.982 1.209 0.9906 -0.0635
rs715350-126_B_R_IFB1136460923:0 A A 0.9414 0.026 1.234 0.0013 0.0776
rs2635442-126_T_R_IFB1136432512:0 G G 0.8315 0.979 0.828 1.0000 -0.0373
rs7055953-123_T_R_IFB1138374757:0 A G 0.7232 0.645 0.733 0.4989 -0.1453
rs7979673-116_B_F_IFB1138390720:0 G G 0.9358 0.995 1.172 1.0000 0.0263
rs6424572-126_B_F_IFB1136436775:0 A A 0.9519 0.013 0.492 0.0064 -0.2712
rs10829026-120_B_F_IFB1136494680:0 G G 0.8892 0.904 0.258 0.9278 -0.0568
rs7037313-126_B_F_IFB1136521486:0 A G 0.8814 0.613 0.855 0.4645 0.1500
rs5920594-114_B_F_IFB1138334897:0 A A 0.8078 0.017 0.819 0.0108 -0.1056
rs16972915-123_B_F_IFB1138342491:0 A G 0.9465 0.594 1.146 0.4900 -0.3071

Total number of rows: 1072820

Table truncated, full table size 75212 Kbytes.




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

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