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Sample GSM566662 Query DataSets for GSM566662
Status Public on Jul 16, 2010
Title BRCA2 Breast tumor 80654 4240263181_B 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 0.568328 1.025744 0.4912941 -0.01680997
rs10000023-126_B_F_IFB1153358872:0 AB 0.8234195 0.4948751 2.064629 0.4979907 -0.2644783
rs10000030-120_B_R_IFB1137703207:0 BB 0.8158658 0.9884899 0.8100064 1 0.06855164
rs1000007-123_T_F_IFB1152225452:0 AA 0.8747823 0.006699079 1.003324 0 0.2023316
rs10000092-123_T_R_IFB1153358875:0 AA 0.9264655 0.0149776 0.8809379 0.007693451 0.2243204
rs10000121-126_B_R_IFB1136471760:0 BB 0.891854 0.9816405 0.5456336 0.9948936 -0.1987295
rs1000014-126_B_R_IFB1136184019:0 BB 0.7254323 0.9555067 1.557004 0.9895598 0.1295311
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.980974 0.9297484 0.993543 0.01779695
rs1000016-126_B_R_IFB1156563530:0 AB 0.875866 0.5265774 1.57027 0.548575 -0.1419213
rs10000169-119_T_R_IFB1135612081:0 AA 0.8703538 0.01307293 0.9177572 0.004903062 -0.1292846
rs1000022-126_B_F_IFB1135126284:0 BB 0.8797732 0.9367762 0.9876515 0.9359609 0.1829903
rs10000272-126_T_R_IFB1136539894:0 AA 0.8433961 0.00507495 1.342546 0.003683744 -0.4926979
rs10000282-121_T_R_IFB1136743500:0 BB 0.8183947 0.983537 0.966577 0.9977875 -0.3143357
rs10000300-126_T_R_IFB1152704058:0 BB 0.8601294 0.9541069 0.661302 0.9916797 -0.09528435
rs1000031-123_B_F_IFB1135583872:0 BB 0.8717313 0.986728 1.49067 0.9987994 -0.0287345
rs1000032-126_B_R_IFB1136145093:0 BB 0.384529 0.9842824 1.325582 1 0.2255574
rs10000388-126_B_F_IFB1135932472:0 BB 0.9530174 0.9904229 1.117701 1 -0.02144725
rs1000040-126_T_F_IFB1152704061:0 AA 0.8484263 0.01915774 1.102037 0.004743229 0.4063836
rs1000041-126_T_F_IFB1153889147:0 BB 0.8351063 0.9702761 1.348271 0.988233 -0.06780886
rs10000432-126_T_R_IFB1135756304:0 BB 0.8544981 0.9884993 0.6899763 1 -0.2212809

Total number of rows: 370404

Table truncated, full table size 30831 Kbytes.




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