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Sample GSM566641 Query DataSets for GSM566641
Status Public on Jul 16, 2010
Title BRCA2 Breast tumor 30184 1922058443_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 BB 0.9368909 0.9940667 0.7260914 1 -0.407474
rs10000023-126_B_F_IFB1153358872:0 BB 0.8234195 0.9777964 1.455099 0.996871 -0.2630906
rs10000030-120_B_R_IFB1137703207:0 BB 0.8158658 0.9936579 0.6732053 1 -0.2047032
rs1000007-123_T_F_IFB1152225452:0 AA 0.8747823 0.01237695 0.7595302 0.003868966 -0.201794
rs10000092-123_T_R_IFB1153358875:0 BB 0.9264655 0.984834 0.6989495 1 0.08563519
rs10000121-126_B_R_IFB1136471760:0 AA 0.891854 0.02044243 0.325221 0.009361411 -0.5389966
rs1000014-126_B_R_IFB1136184019:0 NC 0.04007452 0.2766865 1.938922 0.2779268 -0.1151143
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.9914154 0.9567363 1 0.05602277
rs1000016-126_B_R_IFB1156563530:0 AA 0.875866 0.008342716 1.422466 0.006785854 -0.3216935
rs10000169-119_T_R_IFB1135612081:0 AB 0.7891471 0.5309975 1.382351 0.4113131 0.2099923
rs1000022-126_B_F_IFB1135126284:0 BB 0.8797732 0.9808528 0.9383377 0.9994633 0.1103199
rs10000272-126_T_R_IFB1136539894:0 AA 0.8434824 0.004945165 1.570916 0.003546055 -0.2660552
rs10000282-121_T_R_IFB1136743500:0 BB 0.8183947 0.994427 1.114293 1 -0.1029951
rs10000300-126_T_R_IFB1152704058:0 BB 0.8601294 0.9885246 0.7344617 1 0.05387618
rs1000031-123_B_F_IFB1135583872:0 AB 0.8717313 0.4015249 2.626037 0.4321786 0.1859005
rs1000032-126_B_R_IFB1136145093:0 BB 0.384529 0.9837191 1.466952 1 0.3717943
rs10000388-126_B_F_IFB1135932472:0 AA 0.9530174 0.005174239 1.553557 0 0.1952931
rs1000040-126_T_F_IFB1152704061:0 AA 0.8484263 0.02151199 1.060856 0.006714841 0.3502483
rs1000041-126_T_F_IFB1153889147:0 BB 0.8351063 0.9719879 1.480412 0.9899912 0.0688824
rs10000432-126_T_R_IFB1135756304:0 AB 0.8544981 0.7057891 0.5409408 0.5017707 -0.3830546

Total number of rows: 370404

Table truncated, full table size 30701 Kbytes.




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