Matched Normal Tissue Sample of RNAseq data from TCGA

Question

[rajesh]

Hello Everyone I have downloaded the RNA seq data RSEM normalized from TCGA with the help of TCGA Assembler. When I look for Normal Samples is the downloaded cancer Sample ID, I found that some of the TCGA cancer sample type does not have matched tumor-normal sample. Cancer Type which dont have Matched Normal are - LAML, ACC, LGG, DLBC, MESO, OV, TGCT, UCS, UVM. I have to do the differential gene expression analysis. so my question is from where to get normal sample data for above mentioned cancer types.

Answer 1

[raunakms]

You may use data from GTEx Project selecting the appropriate tissue type. https://gtexportal.org/

[i.sudbery]

I'm not sure how much of a good idea this is - GTEx data was produced using different library preparation techniques, by different labs, on different sources of material and sequenced on different machines. The chances that the two data sets are sufficiently comparable for differential expression analysis is basically zero. You can tell this by taking a cancer that DOES have normal controls in TCGA and clustering the cancer TCGA, the normal TCGA and the GTEx samples. You will see that the TCGA normals do not cluster with the GTEx normals which will cluster very tightly and distantly from anything in TCGA.

[shanthi011]

Hi, can we alternatively use 'Blood Derived Normal' or 'Solid Tissue Normal' for such cases?