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Sample GSM676375 Query DataSets for GSM676375
Status Public on Feb 17, 2011
Title 3519_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 3519_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 3519
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
3519_Child.Score
3519_Child.R
3519_Child.Theta
3519_Child.B Allele Freq
3519_Child.Log R Ratio

Data table
ID_REF VALUE 3519_Child.Score 3519_Child.R 3519_Child.Theta 3519_Child.B Allele Freq 3519_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 3.255708 0.007615477 0.00 -0.5854686
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 2.928839 0.02853335 0.00 -0.6073574
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.266778 0.02689462 0.00 -0.5263812
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 4.606398 0.01268902 0.00 -0.4406165
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 3.70801 0.04754194 0.00 -0.3289014
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 3.489007 0.02652396 0.00 -0.3229086
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.197034 0.06630412 0.007182088 -0.6130528
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 4.418211 0.01913254 0.02503277 -0.99113
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.1734011 0.4777351 0.07255847 0.02679545 -1.68302
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.405533 0.01250317 0.00 -0.302966
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.848809 0.02459798 0.004559587 -0.3260851
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.191996 0.8386297 1 0.7056705
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.219162 0.05685482 0.04945714 -0.3877405
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 3.276451 0.0374856 0.00 -0.2982814
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.515468 0.9629216 1 -0.04366098
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 4.727855 0.00893269 0.00 -0.3148406
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 4.764183 0.01226754 0.00 -0.1502367
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 3.167383 0.0212532 0.00 -0.5437781
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 2.688085 0.0604084 0.00 -0.8847213
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 1.943139 0.01561986 0.00 -0.8880234

Total number of rows: 555352

Table truncated, full table size 45586 Kbytes.




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