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Sample GSM676374 Query DataSets for GSM676374
Status Public on Feb 17, 2011
Title 3094_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 3094_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 3094
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
3094_Child.Score
3094_Child.R
3094_Child.Theta
3094_Child.B Allele Freq
3094_Child.Log R Ratio

Data table
ID_REF VALUE 3094_Child.Score 3094_Child.R 3094_Child.Theta 3094_Child.B Allele Freq 3094_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 2.950038 0.01181087 0.00 -0.7277058
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 2.560402 0.03572765 0.00 -0.8067712
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 2.520292 0.03733016 0.005529996 -0.9006588
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 3.59772 0.0199809 0.002285808 -0.7971727
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2469137 2.591545 0.06190037 0.00 -0.8712502
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 2.736834 0.03074938 0.0007608113 -0.6732172
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 0.8654549 0.05745873 0.00 -1.080986
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 3.617824 0.03259286 0.04085725 -1.280617
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.1958721 0.5289441 0.08270463 0.03880034 -1.536116
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 1.695634 0.02632274 0.007972918 -0.8074974
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.486104 0.03412412 0.01529332 -0.641146
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 2.868855 0.8103537 1 0.1382073
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 3.591627 0.06966508 0.06300142 -0.6200592
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 2.685241 0.04209837 0.00 -0.5853637
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.525124 0.9354459 1 -0.163585
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 3.665313 0.01671924 0.00 -0.68209
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 3.647026 0.02952948 0.008338329 -0.5357452
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 2.419327 0.02978179 0.00 -0.9324634
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 2.653395 0.07951574 0.004459999 -0.9201515
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.035718 0.02665026 0.00 -0.8208747

Total number of rows: 555352

Table truncated, full table size 45800 Kbytes.




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