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Sample GSM676372 Query DataSets for GSM676372
Status Public on Feb 17, 2011
Title 2714_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 2714_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 2714
phenotype: idiopathic MR
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label C-Bio and A-DNP
Label protocol DNA from the proband in each trio was used for hybridization on the Illumina Human Hap550 Beadchips according to the manufacturer’s instructions
 
Hybridization protocol DNA was hybridized overnight to a Beadchip placed in a humidified chamber
Scan protocol Beadchips were imaged using a two-color confocal laser system with 0.8-μm resolution to identify both SNP alleles
Data processing The intensities for each allele were extracted and normalized, and values for genotypes, allelic ratio (B-allele frequency) and logR ratio were calculated using an Illumina-supplied cluster file, which is based on a set of about 100 HapMap reference samples. The normalization algorithm adjusts for nominal offset, cross-talk, and intensity variations observed in the two-color channels. CNV detection was done using PennCNV [20] with a threshold of 5 SNP-minimum per bin
 
Submission date Feb 16, 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 GPL6433
Series (2)
GSE27364 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Illumina HumanHap550)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions
ID_REF
VALUE G Type
2714_Child.Score
2714_Child.R
2714_Child.Theta
2714_Child.B Allele Freq
2714_Child.Log R Ratio

Data table
ID_REF VALUE 2714_Child.Score 2714_Child.R 2714_Child.Theta 2714_Child.B Allele Freq 2714_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 3.290401 0.005754897 0.00 -0.5701764
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 3.020673 0.02828625 0.00 -0.5626289
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.166203 0.02721547 0.00 -0.5714963
MitoA11468G-13273289_B_R_IFB1141719645:0 BB 0.3254292 2.942822 0.9089753 0.9665524 -0.1222181
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 3.565613 0.06131123 0.00 -0.4098745
MitoA12309G-13273294_T_F_IFB1141664161:0 BB 0.256167 2.767642 0.8910111 1 -0.1448315
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.10789 0.1009826 0.04855482 -0.7247016
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 4.462251 0.02004651 0.02610727 -0.9768985
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.1897871 0.5149955 0.07667248 0.03166313 -1.574671
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.275059 0.04548554 0.02926883 -0.3834186
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.506541 0.02556461 0.005648761 -0.6214412
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.505135 0.7956396 1 0.2512982
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.077822 0.05784041 0.0504992 -0.4368979
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 3.0919 0.03212632 0.00 -0.3819214
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.695258 0.9442384 1 -0.03054418
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 4.196709 0.01146628 0.00 -0.4867681
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 4.064102 0.01597697 0.00 -0.3795288
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 2.721398 0.05332348 0.02104196 -0.7627216
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 3.488322 0.06725123 0.00 -0.5147663
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.831063 0.0198381 0.00 -0.3450687

Total number of rows: 555352

Table truncated, full table size 45675 Kbytes.




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

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