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Sample GSM676371 Query DataSets for GSM676371
Status Public on Feb 17, 2011
Title 2569_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 2569_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 2569
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
2569_Child.Score
2569_Child.R
2569_Child.Theta
2569_Child.B Allele Freq
2569_Child.Log R Ratio

Data table
ID_REF VALUE 2569_Child.Score 2569_Child.R 2569_Child.Theta 2569_Child.B Allele Freq 2569_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 2.966457 0.006017052 0.00 -0.7196986
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 2.593309 0.03536128 0.00 -0.7880698
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 2.478131 0.0238494 0.00 -0.9249973
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 3.736445 0.01837395 0.0004827674 -0.7425893
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503373 2.813666 0.05971846 0.00 -0.7487632
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 2.76277 0.02950721 0.00 -0.6596096
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 0.9423238 0.1003746 0.04782944 -0.958222
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 3.665439 0.02144279 0.02774879 -1.260803
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.1669552 0.4630966 0.06935786 0.02300851 -1.727918
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.010031 0.02094968 0.002001763 -0.5621049
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.428788 0.03234997 0.01329428 -0.697889
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 2.908641 0.7997193 1 0.02883652
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 3.512848 0.06313269 0.05609472 -0.6520556
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 2.95619 0.04080514 0.00 -0.4466761
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.435521 0.9529959 1 -0.1368455
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 3.722163 0.01497345 0.00 -0.6598853
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 3.673023 0.01911181 0.00 -0.5254976
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 2.654235 0.02711582 0.00 -0.7987736
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 2.051481 0.08013132 0.005231785 -1.29186
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3107909 1.582712 0.02524603 0.00 -1.184014

Total number of rows: 555352

Table truncated, full table size 45706 Kbytes.




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