RNA Seq and Somatic Calls for the Cancer data

Question

[always_learning]

Dear All,

I am working on a project related to cancer. I have RNASeq data only for tumor samples and matched Tumor/normal samples for WES data. I have performed WES calling on Tumor/Normal Sample. Now I wanted to analyze RNASeq data. Since I don't have matched Normal Control data for RNASeq so I couldn't able to do DE analysis. Could someone please suggest to me what other types of analysis I can perform considering that I have the only tumor RNA-Seq data. I have the RNA seq sample of around 16 patients.

Regards,

[rpolicastro]

What question are you trying to answer?

[always_learning]

This particular cancer is a very rare type so we are trying to see if we can found some gene that may have some role in this using transcriptome data. We have performed somatic calling also and wondering if we can integrate data SNP data with RNA seq also.

Answer 1

[Kevin Blighe]

You could try:

1. Derive FPKM values for your tumour sample
2. Transform to Z-scores via zFPKM package
3. Check expression of genes in 'healthy' tissue from GTEx to gauge tumour-specificity
4. Regress tumour expression Z-scores to nearby mutations / genotypes (nearby in genomic space) via binary logistic regression, i.e., an eQTL analysis.

You could also use data from studies already-published.

Kevin

[always_learning]

Thanks Kevin! I didn't understand point 3 properly. Do you have some reference paper for above so it will be easier for me to follow?.

Thanks

[Kevin Blighe]

Hey, no reference paper specifically (there are probably many), but, for example, if you are studying liver hepatocellular carcinoma, then you would check to see the expression of your gene in healthy liver tissue in GTEx