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Sample GSM676380 Query DataSets for GSM676380
Status Public on Feb 17, 2011
Title 6932_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 6932_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 6932
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) [email protected]
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
6932_Child.Score
6932_Child.R
6932_Child.Theta
6932_Child.B Allele Freq
6932_Child.Log R Ratio

Data table
ID_REF VALUE 6932_Child.Score 6932_Child.R 6932_Child.Theta 6932_Child.B Allele Freq 6932_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 4.812983 0.002435107 0.00 -0.02150843
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 3.946357 0.03003294 0.00 -0.1783034
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 4.411599 0.01848044 0.00 -0.09294825
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 6.868994 0.006890028 0.00 0.1358434
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 5.107853 0.03741652 0.00 0.1514392
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 4.316993 0.01632773 0.00 -0.01569829
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.347876 0.04195191 0.00 -0.4418291
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 6.74755 0.0128887 0.01769227 -0.3796957
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.1672407 0.4637456 0.07440645 0.02898197 -1.725898
MitoA14234G-13273304_T_F_IFB1141674277:0 AB 0.2740649 1.764915 0.5217599 0.5603485 -0.6834604
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 2.003635 0.0218313 0.001442192 -0.2100616
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.578478 0.8374125 1 0.8500921
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 5.446374 0.05485427 0.04734196 -0.01940078
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 4.549672 0.0255215 0.00 0.1753472
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.743405 0.9571038 1 0.05399115
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 6.416611 0.006302729 0.00 0.1257852
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 5.795146 0.008465922 0.00 0.1323794
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 3.891862 0.01721139 0.00 -0.246609
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 4.82632 0.05051983 0.00 -0.03166218
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 3.343354 0.01071937 0.00 -0.1051165

Total number of rows: 555352

Table truncated, full table size 45776 Kbytes.




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