I am working on DNA data (our own experimental data) for some cancer types of human. We only have Fastq data from normal sample without pair tumor sample. I have done variant calling with GATK Tool and get the vcf file (Germline mutations). However, most of cancer research compare information (somatic mutations) about cancer and germline DNA. I want to identify the driver genes (patients can vary the type and severity of possible side-effects) with germline mutations. Now, I only can do some routine analysis (i.e. calculate mutation frequency, annotate variants to genomic features, assess the functional effect , ...). About some tools be used to identify driver genes from a cohort of cancer patients such as MutSigCV, MuSiC, OncodriveFM. Do these tools make the right? Or what is the right tool for the analysis germline mutations? Could anyone share some experience about this issue?
Many thanks !
Andy - Lin
Pharmacogenomics (a portmanteau of pharmacology and genomics) is the study of the role of genetics in drug response. Most patient populations show large interindividual variability in drug response and toxicity (i.e., certain drugs do not work as well as expected, whereas in other patients they cause toxic effects, even at lower doses). For some patients, the reason may be genetic.
I have two group of patients.
The first group doesn't develop toxic effects.
The second group develops toxic effects.
I want to identify the driver genes causing toxic effects (not causing cancer) with germline mutations (SNP, InDel).