A colleague told me that phenol chloroform extraction is not the best and most contemporary way to extract DNA for exome sequencing. One of our sequencing center partners require us to extract DNA using this method. Is phenol chloroform extraction really less desirable and is there a better standard for extracting DNA out there? This question is about DNA from fresh peripheral blood samples where sample amount is not a limiting factor.
Thanks.
1 answer
The biggest downsides to phenol-chloroform are the time required and the fact that you have to work in a hood (well, and dispose of things in a safe manner). The alternative is a column-based kit (e.g., anything from Qiagen). Those are quick and easy and produce good results (normally), but end up being more expensive.
They have good values in terms of purity and concentration and have worked well in sequencing. The only exception to that have been weird tissues, like sperm.
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