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Sample GSM676377 Query DataSets for GSM676377
Status Public on Feb 17, 2011
Title 4821_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 4821_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 4821
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
4821_Child.Score
4821_Child.R
4821_Child.Theta
4821_Child.B Allele Freq
4821_Child.Log R Ratio

Data table
ID_REF VALUE 4821_Child.Score 4821_Child.R 4821_Child.Theta 4821_Child.B Allele Freq 4821_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 3.349333 0.003754739 0.00 -0.5445659
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 3.132783 0.02987622 0.00 -0.5112614
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.222075 0.0210651 0.00 -0.5462595
MitoA11468G-13273289_B_R_IFB1141719645:0 BB 0.3254292 2.507215 0.9424003 1 -0.246416
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 3.522235 0.04519714 0.00 -0.3988455
MitoA12309G-13273294_T_F_IFB1141664161:0 BB 0.256167 2.464317 0.9123284 1 -0.281036
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 0.9675174 0.04595304 0.00 -0.9201574
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 4.601892 0.01723753 0.02280493 -0.9322033
MitoA13781G-13273301_T_F_IFB1141687043:0 NC 0.121038 0.3611041 0.09635483 0.05495118 -2.086816
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.042194 0.01228979 0.00 -0.5392026
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.486597 0.01929888 0.00 -0.6406672
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.156649 0.825219 1 0.4787058
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.461721 0.05193306 0.04425337 -0.3070965
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 2.913894 0.03436559 0.00 -0.4674668
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.490048 0.9418401 1 -0.155529
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 4.731311 0.01036683 0.00 -0.3137864
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 4.195291 0.009785566 0.00 -0.3336948
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 2.929111 0.02445178 0.00 -0.6566067
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 3.344523 0.05749532 0.00 -0.566938
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.619813 0.01721637 0.00 -0.4569491

Total number of rows: 555352

Table truncated, full table size 45939 Kbytes.




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