GDC data only cancer sample without normal sample

Question

[bharata1803]

Hello,

I want to ask about data published in TCGA and now is hosted by GDC data portal. The link is this: LINK. After I check the manifest of the metadata, there are no normal samples. Am I right? I am afraid I made a mistake and if there are no normal sample, where I can download the normal sample? Thank you.

Answer 1

[cindy.perscheid]

Hi bharata, maybe a bit late, but the there exist normal samples in the TCGA data. Not for all studies, though (e.g. not for LAML), but you can use R libraries like TCGAbiolinks to download a customized TCGA data set, e.g. with only normal samples, by specifying the sample type. Have a look here: https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html

By the way, the sample type is also encoded directly into the TCGA barcode: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes

Best,

Cindy

[bharata1803]

Thank you. I have solved this problem. From the new GDC portal, when we have selected all samples that we want to download, we can go to the download cart. From the download cart, we can download the samples metadata. The metadata contains a lot of information about each sample in json format. One of the information is sample type. We can also know which normal-tumor sample comes from same patient. I have written a java code to extract necessary information from the json metadata into csv format. Now, I can directly use it for downstream analysis, for example DESeq2.