I want to download cancer dataset that contains some normal (control) samples too. Right now I can download data from BoradInstitute but I believe the dataset only contains cancerous patients information. For example, I need to download Breast cancer methylation dataset where I can have methylation state of both cancer patient and normal sample. Can anyone give me direction for downloading such data?
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
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