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sample of choice for non-tumor DNA

NGS non-tumor

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5 replies to this topic

#1 ramblingrat

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Posted 24 June 2012 - 04:20 AM

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!! :o)

All the best,
the rat

#2 leelee

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Posted 24 June 2012 - 08:05 PM

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?

#3 ramblingrat

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Posted 25 June 2012 - 10:13 AM

hi leelee,

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

#4 leelee

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Posted 25 June 2012 - 06:35 PM

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?

#5 ramblingrat

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Posted 15 July 2012 - 01:21 PM

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.

#6 leelee

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Posted 15 July 2012 - 06:54 PM

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 :)





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