Question: Cancer data download with normal sample
gravatar for mhasa006
3 months ago by
United States
mhasa00640 wrote:

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?

cancer cancer data tcga normal • 241 views
ADD COMMENTlink modified 3 months ago by Kevin Blighe41k • written 3 months ago by mhasa00640
gravatar for Kevin Blighe
3 months ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k wrote:

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

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 | sed 's/\t/\n/g' | head -10
Hybridization REF

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 | sed 's/\t/\n/g' | grep -e "11$"  | wc -l


ADD COMMENTlink modified 3 months ago • written 3 months ago by Kevin Blighe41k
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