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Fast, cheap and dummy proof large scale DNA extraction? - (Feb/05/2009 )

I work in a biobank storing breeding animal samples. One of our customers has just presented a possible project for 2010 which will include DNA extraction from approx 10 000 muscle tissue samples. DNA is supposed to be used for marker assisted selection/Sequenom -SNP typing.

Our lab uses the MagNA Pure LC extractor which gives DNA of very high quality. The drawback is that the price per sample also is more than our customer is willing to give. some colleagues have work experience with the 96 deep well DNeasy system, which works fine. However, our customer still finds the sample price with that system too high. so now I have to search for something that is cheaper and fast and possible to upscale -which means that it should be as close to dummy proof as possible. With 10 000 samples we can't risk switching tubes or labels or simply dropping a rack of tiny unmarked tubes to the ground.

Has anybody on here any experience with such a large scale and cheap extraction system, kit based or not? our customer has informed that the DNA concentration might not be higher than 10ng/Ál.

Would it be possible to simply lyse the muscle cells and do MAS directly on the lysate?

-DocFlow-

DocFlow on Feb 5 2009, 06:56 AM said:

I work in a biobank storing breeding animal samples. One of our customers has just presented a possible project for 2010 which will include DNA extraction from approx 10 000 muscle tissue samples. DNA is supposed to be used for marker assisted selection/Sequenom -SNP typing.

Our lab uses the MagNA Pure LC extractor which gives DNA of very high quality. The drawback is that the price per sample also is more than our customer is willing to give. some colleagues have work experience with the 96 deep well DNeasy system, which works fine. However, our customer still finds the sample price with that system too high. so now I have to search for something that is cheaper and fast and possible to upscale -which means that it should be as close to dummy proof as possible. With 10 000 samples we can't risk switching tubes or labels or simply dropping a rack of tiny unmarked tubes to the ground.

Has anybody on here any experience with such a large scale and cheap extraction system, kit based or not? our customer has informed that the DNA concentration might not be higher than 10ng/Ál.

Would it be possible to simply lyse the muscle cells and do MAS directly on the lysate?


Our AquaGenomic may be the right product for you. Adding proteinase k in AquaGenomic and incubating for 90min to extract DNA, you will not need to use homogenizers and avoid cross-contamination. Here's the protocol. We'd be happy to work with you on high throughput and pricing.

-AquaPlasmid-

I never tried, but look at this Finnzyme product; It sounds really nice and easy.....sadly its not applicable for my samples :( but the Enzymes are great!

I do not know where you are from, but usually they supply samples ;)

-gebirgsziege-

gebirgsziege on Feb 6 2009, 03:00 PM said:

I never tried, but look at this Finnzyme product; It sounds really nice and easy.....sadly its not applicable for my samples :( but the Enzymes are great!

I do not know where you are from, but usually they supply samples :P


Thanks to both of y'all. I'll check with finnzymes. I have great experience with them from my PhD.

I have to check with my customer what "cheap extraction" means to him, because I am worried that the benefit of cheaper and more manual extraction methods will somewhere be lost because of the higher risk of human error. Maybe the answer simply is to negotiate a fair and cheaper price with roche for kits to our extractor.

-DocFlow-

I have to check with my customer what "cheap extraction" means to him,

Watch out!!! He might want triagent :lol:



Maybe the answer simply is to negotiate a fair and cheaper price with roche for kits to our extractor.

Always the best thing to do!!! ;)

-molgen-

molgen on Feb 12 2009, 05:16 PM said:

I have to check with my customer what "cheap extraction" means to him,

Watch out!!! He might want triagent :)



Maybe the answer simply is to negotiate a fair and cheaper price with roche for kits to our extractor.

Always the best thing to do!!! :D


Yup, I've been negotiating with roche and I belive we have got a fair price. I'll take it from there and present a fair price to our customer. I don't want to spend lots of time searching and testing new methodology for these samples as long as we initially have a fair price with Roche. I'll keep you all updated... ;)

Hey, molgen. Are you from Norway too? Your nick looks like a shortening of mole genetics, LOL

-DocFlow-

Accidently had a human sample to do last week....worked great with the finnzymes direct PCR protocol.

But I agree if you have a good price for your extractor and know it works...never change a winning team :blink:

-gebirgsziege-