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Sample GSM676367 Query DataSets for GSM676367
Status Public on Feb 17, 2011
Title 1780_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 1780_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 1780
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
1780_Child.Score
1780_Child.R
1780_Child.Theta
1780_Child.B Allele Freq
1780_Child-DNA#C05.Log R Ratio

Data table
ID_REF VALUE 1780_Child.Score 1780_Child.R 1780_Child.Theta 1780_Child.B Allele Freq 1780_Child-DNA#C05.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 3.495077 0.006781009 0.00 -0.4831152
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 2.990287 0.03056615 0.00 -0.5789458
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.335993 0.03642485 0.00449741 -0.4961337
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 5.173605 0.01483244 0.00 -0.2730856
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 3.517851 0.05421011 0.00 -0.4167581
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 3.092922 0.02205112 0.00 -0.4967546
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.035438 0.08856098 0.03373537 -0.8222764
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 5.253943 0.0240992 0.03087178 -0.741615
MitoA13781G-13273301_T_F_IFB1141687043:0 NC 0.1453379 0.4134878 0.06861866 0.02213388 -1.891386
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.162705 0.01364031 0.00 -0.4564857
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.588558 0.01512902 0.00 -0.5449634
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.347037 0.7843093 1 0.06251772
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.235711 0.06390563 0.05691195 -0.3820927
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 3.31993 0.03830958 0.00 -0.2792625
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.360947 0.9351971 1 -0.2616615
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 4.750043 0.01225998 0.00 -0.3080858
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 4.409485 0.01123838 0.00 -0.2618552
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 2.883245 0.02523455 0.00 -0.6793758
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 3.811398 0.05735162 0.00 -0.3782917
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.95294 0.02035224 0.00 -0.2842608

Total number of rows: 555352

Table truncated, full table size 45770 Kbytes.




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