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Sample GSM676379 Query DataSets for GSM676379
Status Public on Feb 17, 2011
Title 6428_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 6428_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 6428
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
6428_Child.Score
6428_Child-DNA#C06.R
6428_Child.Theta
6428_Child.B Allele Freq
6428_Child.Log R Ratio

Data table
ID_REF VALUE 6428_Child.Score 6428_Child-DNA#C06.R 6428_Child.Theta 6428_Child.B Allele Freq 6428_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 3.462583 0.005920355 0.00 -0.4965911
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 3.539334 0.03026649 0.00 -0.3355244
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.657599 0.02961845 0.00 -0.3633527
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 5.096356 0.01932185 0.001546339 -0.2947893
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 3.924155 0.05018513 0.00 -0.2518957
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 3.663078 0.02690713 0.00 -0.2526687
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.238768 0.06605519 0.006885113 -0.5636104
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 4.877137 0.02158768 0.02791914 -0.8487669
MitoA13781G-13273301_T_F_IFB1141687043:0 NC 0.1377831 0.3957915 0.08635807 0.04312307 -1.95449
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.375165 0.01434364 0.00 -0.321295
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.635709 0.01833238 0.00 -0.5027652
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.522505 0.8172165 1 0.5243391
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.950067 0.06236811 0.05528634 -0.1572489
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 3.617101 0.03855548 0.00 -0.1555815
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.909677 0.9342018 1 0.03548947
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 4.696069 0.01239035 0.00 -0.3245727
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 4.828257 0.0113621 0.00 -0.1309631
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 3.137163 0.02690073 0.00 -0.557609
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 4.009058 0.05976644 0.00 -0.3074727
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.801348 0.01776377 0.00 -0.3602915

Total number of rows: 555352

Table truncated, full table size 45462 Kbytes.




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

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