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Sample GSM566634 Query DataSets for GSM566634
Status Public on Jul 16, 2010
Title BRCA2 Breast tumor 20447 1922058188_A DNA
Sample type genomic
 
Source name kConFab
Organism Homo sapiens
Characteristics tissue: Breast Tumour
mutation status: BRCA2
Extracted molecule genomic DNA
Extraction protocol Frozen sections of 10 um were macrodissected with a needle to ensure that the neoplastic content was >75%. DNA was extracted by the salting-out method followed by a phenol chloroform extraction
Label C-Bio and A-DNP
Label protocol Standard Illumina Infinium protocol
 
Hybridization protocol Standard Illumina hybridization protocol to CNV370 duo beadarrays
Scan protocol Standard Illumina scanning protocol
Description n/a
Data processing The samples were preprocessed in Illumina's Genomestudio
 
Submission date Jul 15, 2010
Last update date Jul 15, 2010
Contact name Nic Waddell
Organization name Queensland Centre for Medical Genomics
Street address St Lucia
City Brisbane
ZIP/Postal code 4072
Country Australia
 
Platform ID GPL6986
Series (1)
GSE19177 Subtypes of familial breast tumors revealed by expression and copy number profiling

Data table header descriptions
ID_REF
VALUE genotype call
GC_SCORE
Theta
R
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
rs10000010-126_B_F_IFB1153208421:0 AB 0.9368909 0.5087476 1.131042 0.4397665 0.1380475
rs10000023-126_B_F_IFB1153358872:0 AB 0.8234195 0.5171444 2.042857 0.5210697 -0.261658
rs10000030-120_B_R_IFB1137703207:0 BB 0.8158658 0.9947496 0.6035619 1 -0.3635893
rs1000007-123_T_F_IFB1152225452:0 AA 0.8747823 0.007742522 0.9444028 0.000301588 0.1145553
rs10000092-123_T_R_IFB1153358875:0 AA 0.9264655 0.008934004 0.6604443 0.001576158 -0.1916133
rs10000121-126_B_R_IFB1136471760:0 AB 0.891854 0.6476229 0.426231 0.4983754 -0.3986243
rs1000014-126_B_R_IFB1136184019:0 AA 0.7254323 0.05251353 2.261154 0.009800303 0.1482981
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.9951128 0.8903483 1 -0.04880913
rs1000016-126_B_R_IFB1156563530:0 AA 0.875866 0.007614127 1.344846 0.006018261 -0.4026453
rs10000169-119_T_R_IFB1135612081:0 AA 0.8703538 0.01244381 1.122709 0.0044094 0.1618485
rs1000022-126_B_F_IFB1135126284:0 BB 0.8797732 0.9862673 0.8502203 1 -0.0318001
rs10000272-126_T_R_IFB1136539894:0 AA 0.8434824 0.002896276 1.677472 0.001372394 -0.1712483
rs10000282-121_T_R_IFB1136743500:0 BB 0.8183947 0.9917834 1.169477 1 -0.03475982
rs10000300-126_T_R_IFB1152704058:0 BB 0.8601294 0.9931172 0.9104372 1 0.3634529
rs1000031-123_B_F_IFB1135583872:0 BB 0.8717313 0.9871747 1.375136 0.9992259 -0.1444726
rs1000032-126_B_R_IFB1136145093:0 BB 0.384529 0.9960949 1.373654 1 0.2760845
rs10000388-126_B_F_IFB1135932472:0 AB 0.9521666 0.4041505 1.480364 0.388115 0.08855648
rs1000040-126_T_F_IFB1152704061:0 AB 0.8484263 0.6277618 1.240435 0.5230037 0.3102379
rs1000041-126_T_F_IFB1153889147:0 AB 0.8351063 0.5387791 1.789968 0.5450331 -0.05396517
rs10000432-126_T_R_IFB1135756304:0 BB 0.8544981 0.9831983 0.6764908 1 -0.2464271

Total number of rows: 370404

Table truncated, full table size 30335 Kbytes.




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