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Sample GSM676373 Query DataSets for GSM676373
Status Public on Feb 17, 2011
Title 2894_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 2894_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 2894
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
2894_Child.Score
2894_Child.R
2894_Child.Theta
2894_Child.B Allele Freq
2894_Child.Log R Ratio

Data table
ID_REF VALUE 2894_Child.Score 2894_Child.R 2894_Child.Theta 2894_Child.B Allele Freq 2894_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 4.290124 0.004045838 0.00 -0.1874203
MitoA10551G-13273286_T_F_IFB1141639111:0 BB 0.6703396 1.903276 0.9408623 0.9867661 -1.331446
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.975434 0.01708268 0.00 -0.2431373
MitoA11468G-13273289_B_R_IFB1141719645:0 BB 0.3254292 2.481723 0.9412568 1 -0.2649522
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 4.369995 0.04071942 0.00 -0.07963097
MitoA12309G-13273294_T_F_IFB1141664161:0 BB 0.256167 2.380642 0.8990548 1 -0.3504203
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.347171 0.07598855 0.01873598 -0.4425839
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 6.023334 0.01691796 0.02242923 -0.543841
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.167387 0.4640782 0.06055394 0.01259175 -1.724863
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.586789 0.01038455 0.00 -0.1981602
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.779495 0.01160772 0.00 -0.3812134
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.3378 0.7937619 1 0.1597465
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.824454 0.04479198 0.03670312 -0.194331
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 3.941749 0.03124463 0.00 -0.03157929
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.440034 0.9496781 1 -0.1494175
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 6.176004 0.008955209 0.00 0.07064721
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 5.592039 0.007009486 0.00 0.08090875
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 3.250652 0.02155088 0.00 -0.5063402
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 4.235955 0.05656866 0.00 -0.2252354
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.91619 0.01582755 0.00 -0.3023281

Total number of rows: 555352

Table truncated, full table size 45262 Kbytes.




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