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Sample GSM676366 Query DataSets for GSM676366
Status Public on Feb 17, 2011
Title 1511_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 1511_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 1511
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
1511_Child.Score
1511_Child.R
1511_Child.Theta
1511_Child.B Allele Freq
1511_Child.Log R Ratio

Data table
ID_REF VALUE 1511_Child.Score 1511_Child.R 1511_Child.Theta 1511_Child.B Allele Freq 1511_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3034786 2.614654 0.01168964 0.00 -0.9018195
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 2.118324 0.04232333 0.006545373 -1.085201
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 2.355414 0.02784443 0.00 -0.9982693
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 3.323924 0.02261098 0.005236828 -0.9113683
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 2.831028 0.06599986 0.00 -0.7509397
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.256167 2.675792 0.02235034 0.00 -0.7057593
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.154819 0.09613175 0.0427676 -0.6648501
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554368 3.289681 0.03015971 0.03799674 -1.417585
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.1722326 0.475083 0.08740308 0.04435952 -1.691051
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 1.839304 0.02481111 0.006293022 -0.6901628
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.399665 0.0325332 0.01350073 -0.7275993
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 2.793749 0.7971869 1 -0.05844852
MitoA15219G-13273311_T_F_IFB1141717824:0 BB 0.2522812 2.632402 0.8955575 1 -0.2690651
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 2.509793 0.03771551 0.00 -0.6828467
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.261581 0.9367105 1 -0.3170671
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 3.376283 0.01791224 0.00 -0.8005903
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.2995931 2.927913 0.02270813 0.0006267304 -0.8525929
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 2.141794 0.02974836 0.00 -1.10825
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 2.54671 0.07805307 0.002626177 -0.9780858
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.041622 0.02639516 0.00 -0.8166966

Total number of rows: 555352

Table truncated, full table size 45719 Kbytes.




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