Saturday, July 27, 2019

DNA sequencing

You can find a good overview in Wikipedia.

A bit more in detail, the most used approach today (2020) by far is Illumina's. Also called SBS (sequence by synthesis), it belongs to the 2nd generation technologies (there are others, like Thermofisher's...), ironically called also NGS (next generation sequencing) because it was once the next generation :). It has its drawbacks (high investment upfront...) but it works.

From an electronics perspective, the detection method here is a high speed camera.

Moving fwd, "A world of opportunities with nanopore sequencing" gives a good overview on the latest (a bit centered on Oxford Nanopore Technologies' solution). These are called "long read", as, unlike Illumina's, it can read a long strand of DNA while Illumina's is limited to ~100bp that then you have to "glue" together with the others to get the whole thing. Nanopores have other advantages (portability, immediate results, less reagents, potentially lower cost...) and some issues, like less accurate (although they seem to be addressing this), but it is not clear they'll be able to displace Illumina. It is a bit like PoC vs centralize lab model.

From an electronics perspective, we measure very small variations on current levels (pA) although some different pore technologies may result on larger currents. If you want to get a bit more insight on the electronics for the nanopore technologies (and still get a good overview of the previous generations), check "Nanopore-CMOS Interfaces for DNA Sequencing" out.

A hardcore Nature paper "Integrated nanopore sensing platform with sub-microsecond temporal resolution" on nanopore electronics noise.

Just a last note. DNA sequencing cannot be replaced on some areas, for some tasks. Nevertheless, one does not need to sequence the whole DNA to do things like finding if an illness is coming from a given virus (see qPCR), if someone is the father of the baby, or to find out that one is the carrier of a "cancer gene"... There are more cost effective methods to do that, still based on DNA/RNA.

Books:
  1. "Molecular Cloning: a Laboratory Manual" is not something that you want to read (I haven't, that's just the index, not online) just for basic learning. Instead is mentioned on the first article as the in depth reference for the basic techniques used for DNA manipulation/preparation...
  2. Single-Channel Recording. Sakmann, B.; Neher, E. Springer; 2009
  3. Ion Channels of Excitable Membranes

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