I need to check whether some mutations predicted by computational approaches as drivers are actually driver mutations. What are the best experimental (in vitro or in vivo) for testing this? Would cell viability assays, anchorage dependence assays and Western blotting be sufficient to prove this or are there some better techniques?
In somatic genomes, delineating genuine driver mutations against a background of multiple passenger events is a challenging task. The difficulty of determining function from sequence data and the low frequency of mutations are increasingly hindering the search for novel, less common cancer drivers. The accumulation of extensive amounts of data on somatic point and copy number alterations necessitates the development of systematic methods for driver mutation analysis.
Check this Reference:
Article Distinguishing between driver and passenger mutations in ind...
Best luck
Hi Vidya Warrier
This might be of some interest to you. Not as an answer to your question, but as a source of ideas to consider.
Passengers may not necessarily be neutral. Generally, if you have mutations, mutations usually make cells less fit, make them sort of sick. So what my group is interested in is trying to understand where the passenger mutations may actually be damaging to cancer. Nevertheless, by virtue of cancer sitting and waiting for the next driver and drivers playing the main role in this process, damaging passengers can sort of hitchhike on the driver. And ‘hitchhike’ is not only a metaphorical word here, but it’s actually the name of the genetic process, in which mutations that are not responsible for a specific phenotype can nevertheless sort of propagate jointly with some mutations that lead to a phenotype. In this case cancer cells would accumulate sort of passenger mutations, which might be somewhat damaging. And then one of them would get the driver mutation and found a new population carrying all the baggage of damaging drivers with it.
We hypothesize that they are damaging, but we don’t know to what extent they are damaging, this needs to be tested experimentally. Again, we can do genomic analysis and simulations, but experiments on cells and small animals will actually tell us this. We would like to see whether the number of mutations is actually prognostic of the course of the disease. Some cancers will have more mutations, some less. So what’s the effect of these passenger mutations on the actual progression of the disease? And we would also like to see whether types of passenger mutations – because there might be several types of passenger mutations, right now we put them all together – so whether types of passenger mutations may actually determine phenotype of cancer cells. Some mutations would make them look different, some mutations will make the cells more sick. And finally, we would like to know what are the biological mechanisms that allow cells to evolve while accumulating these bad mutations. We see that there are bad mutations, we see that cancers accumulate them, we don’t know how it manages to live with this load of passenger mutations.'
http://serious-science.org/driver-and-passenger-mutation-in-cancer-3125
I agree with Dr. Ayoob. The attached resource is also very useful. Best regards
Hi vidya !
If the mutation is found at the most conservative region ( i.e, most conserved amino acid in the sequence) but the changed amino acid is not conservative (i.e, changed amino acid is not similar in nature with the replaced amino acid like basic for basic, acidic for acidic, hyrophobic for hydrophobic and so on ) then the mutation is likely a driver one and its oppsite case is mostly known for passenger mutations.
Hope it will help you, best of luck.
So u can go for sequencing to confirm it and then for bioinformatics tools to see the impact of these mutations on conformation and activity.
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