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Sample GSM694407 Query DataSets for GSM694407
Status Public on Jun 30, 2011
Title NA18980 rep2 at TCAG (Human1Mv1_C)
Sample type genomic
 
Source name NA12239
Organism Homo sapiens
Characteristics cell line: GM18980
genotyping center: TCAG
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA12239
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 A G 0.8100 0.626 1.015 0.5070 0.1161
rs3916934-123_B_F_IFB1136503411:0 A G 0.9114 0.626 0.740 0.5125 -0.2525
rs2711935-126_T_R_IFB1138365211:0 A A 0.9032 0.025 1.167 0.0083 -0.2637
rs17126880-123_T_R_IFB1140054009:0 G G 0.9278 0.984 1.252 1.0000 0.1125
rs12831433-126_B_F_IFB1138385824:0 A A 0.8485 0.028 2.073 0.0047 -0.0502
rs12797197-126_B_F_IFB1138411445:0 A A 0.8584 0.059 0.363 0.0089 0.0502
rs11002902-126_B_R_IFB1138389502:0 A G 0.7966 0.425 2.576 0.5403 -0.2205
rs3924674-126_T_R_IFB1136512840:0 G G 0.8702 0.984 0.564 1.0000 0.0561
rs2147587-126_T_F_IFB1154866225:0 A A 0.9660 0.022 0.971 0.0169 -0.2139
rs11983370-126_T_R_IFB1140050766:0 A A 0.7943 0.026 2.382 0.0103 0.0191
rs7167305-126_T_R_IFB1138332395:0 A C 0.8901 0.555 1.372 0.5279 -0.1667
rs715350-126_B_R_IFB1136460923:0 A A 0.9414 0.030 1.533 0.0061 0.3895
rs2635442-126_T_R_IFB1136432512:0 G G 0.8315 0.990 0.816 1.0000 -0.0609
rs7055953-123_T_R_IFB1138374757:0 A A 0.7232 0.008 0.663 0.0016 0.3238
rs7979673-116_B_F_IFB1138390720:0 G G 0.9358 0.992 1.068 1.0000 -0.1092
rs6424572-126_B_F_IFB1136436775:0 A A 0.9519 0.019 0.425 0.0120 -0.4844
rs10829026-120_B_F_IFB1136494680:0 G G 0.8892 0.982 0.360 1.0000 0.4389
rs7037313-126_B_F_IFB1136521486:0 A A 0.8814 0.040 0.820 0.0051 0.3451
rs5920594-114_B_F_IFB1138334897:0 A A 0.8078 0.009 0.994 0.0047 0.1795
rs16972915-123_B_F_IFB1138342491:0 G G 0.9465 0.998 1.065 1.0000 -0.1463

Total number of rows: 1072820

Table truncated, full table size 75250 Kbytes.




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

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