Wednesday, 15 July 2015

How should I store my NGS data: disc, tape or tube

Genomics has recently been singled out as one of the largest data headaches we face. As we move to sequencing people multiple times, start newborn genome sequencing programs and increase our use of consumer genomics the amount of data goes up and up. Our GA1 generated 1Gb of data in about 11 days. Today our HiSeq 2500 puts out 1TB in 6.

We're currently storing our data on disc for up to six months. After this we either delete it or archive it onto tape (although Ive no idea if we ever try to get it back off the tapes). A while back people used to talk about the storage being more expensive that a rerun, and I wonder if we are getting even closer to that point, especially if you try to grab the data off a tape in a secure storage facility.

I've always liked the idea of storing libraries and we have all 10,000 that we've run safely stored at -80C. These tubes take minimum space and most could be rerun today at a fraction of the cost from a few years ago. I am now wondering if we should go for an even greener solution and start the long term storage on Whatman cards (available from CamLab and others). A small number of cards could store almost everything we've ever run!

Is anyone doing this?


1 comment:

  1. Competing interests exits!
    I work for one of the two companies that offer chemical products for the protection and storage of DNA, RNA and raw blood, GenTegra LLC. The other company is named Biomatrica.
    Storage of libraries or purified DNA on paper is not something we recommend even though we have a product that uses FTA-paper. FTA paper is designed to preserve the DNA in raw blood samples.
    FTA paper from Whatman (now GE) has been available for decades and was initially designed to protect the DNA from raw blood when spotted on the paper. The FTA chemistry was primarily designed to lyse the red blood cells and to prevent microbial growth and prevent the DNA from being destroyed. The trouble with this method is the DNA is difficult to remove from the paper. If you have libraries or purified DNA you will lose a significant amount by putting it on paper after it has been purified.
    Purified DNA could be added to plain filter paper i.e. Whatman 903 but there is no protection for the DNA and the paper should be stored at -20 or -80. Recovering the DNA will still be a issue.
    If you want to store purified DNA without the environmental impact of freezers and not lose sample on paper, the better approach is to use a chemical matrix that is designed to protect the purified DNA without refrigeration. There are two products available for storing purified DNA, GenTegra-DNA and DNAstable.
    If you want to store DNA without freezing investigate these technologies, they are superior to putting purified DNA on paper matrix.

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