What clinical sample extraction procedures do you usually use for metagenomic sequencing analysis? I have read some papers that use filtration, centrifugation, and nuclease digestion... is it routine for you to use any of these methods?
That really depends on what type of material you have, and what research questions you are asking. E.g., processing a buccal swab will be very different from say processing sea water; same for compositional vs functional analysis etc.
These are clinical serum samples for viral investigation by metagenomic sequencing.
This is not a direct question to answer. Also, they are two different things.
1. DNA extraction
2. Sequencing
Different protocols/kits can be used and the DNA amount and quality will be dependent on the sample attributes.
That DNA (good or bad), then can be used for different type of sequencing. PCR based methods for sequencing are generally more flexible and less dependent on the DNA quality. However, long-read methods can suffer due to poor quality.
So, I think optimization of extraction is not dependent on what the DNA will be used for. Rather, what method will be used for sequencing.
Bead beating of sample disruption is primarily the main cause of DNA fragmentation and bad quality, followed by inhibitors. In serum samples, i think there are no so many inhibitors, so the DNA fragmentation is contributing the most.
Now, for specific case like you mentioned, i.e. viral DNA. Since viral DNA / genome is a small and its incorporation in host genome is random, I don't think it will be a huge difference in DNA quality and bad state of DNA fragmentation.
However, everything is subjective and depends on respective factors. So, I can't draw a general conclusion and provide you with direct answer.
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