There are definitely normal methylation samples for BRCA (and other cancers in TCGA). The file that you likely want from HERE is called gdac.broadinstitute.org_BRCA.Methylation_Preprocess.Level_3.2016012800.0.0.tar.gz. This contains the normalised methylation beta (β) values for all BRCA samples. Within the downloaded tar.gz file, these normalsied values are stored in the file BRCA.meth.by_mean.data.txt.
Here's what this contains:
Hybridization REF TCGA-3C-AAAU-01 TCGA-3C-AALI-01 TCGA-3C-AALJ-01 TCGA-3C-AALK-01
Composite Element REF Beta_Value Beta_Value Beta_Value Beta_Value
A1BG 0,4837161197 0,6371912261 0,6560923982 0,6151944714
A1CF 0,2958272035 0,4589729986 0,4897252896 0,6257652232
A2BP1 0,1876998696 0,2405158477 0,2790878512 0,4888885105
A2LD1 0,6295855132 0,6662722887 0,7556305 0,7457512129
A2M 0,5596536616 0,6075048697 0,662360104 0,7279819032
A2ML1 0,8354122558 0,8423905626 0,8290204696 0,8353647495
A4GALT 0,4848002856 0,5500468176 0,4761066997 0,5560164612
A4GNT 0,6902167979 0,7498897004 0,6537560771 0,6520049818
AAA1 0,8078049982 0,3952904662 0,7951015988 0,8164225961
AAAS 0,1373555163 0,0561035293 0,0677840275 0,0630021045
[NB - I'm in a Latin locale, so, my decimal points are commas]
With regard to how to identify the normals, in this case it is easy. Look at the TCGA barcodes in this file:
head -1 BRCA.meth.by_mean.data.txt | sed 's/\t/\n/g' | head -10
Hybridization REF
TCGA-3C-AAAU-01
TCGA-3C-AALI-01
TCGA-3C-AALJ-01
TCGA-3C-AALK-01
TCGA-4H-AAAK-01
TCGA-5L-AAT0-01
TCGA-5L-AAT1-01
TCGA-5T-A9QA-01
TCGA-A1-A0SB-01
The final number in these [shortened] TCGA barcodes indicate the tissue/sample type:
- 01 to 09 = tumour
- 10 to 19 = normal
- 20 to 29 = control
See here: Meaning letters in TCGA sample barcode field
How many are there? - even just looking for the 11 sample code, we can see that there are at least 97 normal methylation samples in this dataset:
head -1 BRCA.meth.by_mean.data.txt | sed 's/\t/\n/g' | grep -e "11$" | wc -l
97
Kevin
