TCGA-COAD: Mutation prediction from WSI

Question

[math27182]

hi all :)

I need some help finding annotations for the TCGA-COAD dataset (im not a bioinformatician). I have WSIs from TCGA-COAD and I want to do a mutation prediction task from these WSIs (e.g.: paper from Kather ) . However, I have no idea where I can find annotations for mutations (like TP53) for my slides, they should be somewhere on GDC tho. Any help is highly appreciated since I'm trying to figure out how to get them for hours now :(

Answer 1

[Zhenyu Zhang]

Are you talking about MAF files? https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-COAD%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_format%22%2C%22value%22%3A%5B%22maf%22%5D%7D%7D%5D%7D