sample of choice for non-tumor DNA - (Jun/24/2012 )

Hello everyone,

I am designing a project involving non-tumor DNA. We intend to do whole genome sequencing. So I was wondering what would be the sample of choice? Buccal swab? Saliva? Chewing gum? Mouthwash?
Do I get enough material for next generation sequencing from these?
What are the considerations (smokers)?
Which are the pros and cons of there different methods (swab vs. saliva vs. other)?

Since I have no experience with NGS and isolation of DNA from such tissues any help/advise would be appreciated!! )

All the best,
the rat

Just a question- is the non tumour DNA that you are wanting to isolate and sequence to be used as a comparison for tumour DNA?

hi leelee,

yes, it is and the tumor is leukemia, so it should not be anything using blood cells or being contaminated with it.

Why should it not be blood cells? I would have thought the best control for cancerous cells would be their non-cancerous counterpart, so you would actually want blood cells?

Am I missing something?

Hey, thanks for your thoughts. Actually the microenvironment plays a major role in leukemias, therefore "non-tumor" blood cells are a bad choice because they are often mutated as well and consequently a relevant co-factor in tumor-progression.

Ah ok, that makes sense.

In that case, I think you could go with buccal cells. I know that when I teach undergrads and we isolate DNA in this way, we get plenty, so you should be able to get enough. We get them to scrape their inside cheek with a plastic spoon, then proceed to isolate the DNA from their. Its really gross, but effective