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Sample GSM676365 Query DataSets for GSM676365
Status Public on Feb 17, 2011
Title 1056_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 1056_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 1056
phenotype: idiopathic MR
gender: Female
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
1056_Child.Score
1056_Child.R
1056_Child.Theta
1056_Child.B Allele Freq
1056_Child.Log R Ratio

Data table
ID_REF VALUE 1056_Child.Score 1056_Child.R 1056_Child.Theta 1056_Child.B Allele Freq 1056_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 4.232519 0.008134331 0.00 -0.206923
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 3.381881 0.02197678 0.00 -0.3948711
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.732573 0.02889018 0.00 -0.3340793
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 5.795378 0.01697003 0.00 -0.1093527
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 4.078213 0.04454366 0.00 -0.1862239
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 3.424477 0.02376489 0.00 -0.3498414
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.323881 0.08962755 0.03500783 -0.4677432
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 5.603734 0.02044904 0.0265805 -0.648316
MitoA13781G-13273301_T_F_IFB1141687043:0 BB 0.2118977 0.5663368 0.9845317 1 -1.437571
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.200585 0.01327061 0.00 -0.4314356
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.69128 0.01590915 0.00 -0.4545652
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.744164 0.7513709 0.9901682 -0.08150741
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.833648 0.05567821 0.04821311 -0.1915843
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 3.706531 0.03873819 0.00 -0.1203458
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.473341 0.9270645 1 -0.2296724
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 5.457547 0.01187374 0.00 -0.1077737
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 3.721877 0.009451938 0.00 -0.5064351
MitoA15925G-13273318_T_F_IFB1141694300:0 BB 0.3220414 2.081089 0.9685918 1 -0.5205599
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 2.860976 0.05853342 0.00 -0.7931446
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.414548 0.01574755 0.00 -0.5746595

Total number of rows: 555352

Table truncated, full table size 45519 Kbytes.




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