TCGA samples

Question

[mrashad]

Dears, I am working on the TCGA-LAML project and make a differential expression analysis between cases and control, but while open the sample sheet, I didn't find control samples, please find the attached photo for samples of sample ID and sample type in the sample sheet

So anyone can help how can I get the control samples for this project ?

Answer 1

[Kevin Blighe]

These samples are bone marrow aspirates. There are, indeed, neither matched healthy control samples nor matched normal tissue samples from the blood or marrow of each patient for this cohort; however, within the cohort are 'normal' cytogenetic abnormality sub-types. In this way, the within-cohort comparison could be conducted across sub-types (comparisons against 'normal'). More information on this is in the clinical data: https://portal.gdc.cancer.gov/files/c07a64a0-7588-4653-95ef-982b41a1a804

Otherwise, if you want a true healthy control, you may have to search public studies and download the raw data.

Kevin

[mrashad]

Thanks for this fruitful answer, it helps me a lot