Using nanopore sequencing to look at the diagnostic CLL genome.

[Jm954]

This is a bit sciencie but might be of interest to some and looks promising technology, allowing several things to be tested for at the same time.

Nanopore sequencing is a third generation approach used in the sequencing of biopolymers in the form of DNA or RNA. Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the need for PCR amplification or chemical labeling of the sample.

Current conventional methods, including fluorescent in-situ hybridisation and Sanger sequencing, exhibit shortcomings in terms of cost, speed and sensitivity, and even second-generation sequencing methods encounter technical limitations.

In this paper, they present a nanopore-based CLL-specific screening assay, to simultaneously screen for both TP53 mutations and del17p13.1, as well as determining the IgHV mutation status for a single patient in one sequencing run.

It's only a short abstract but interesting: biorxiv.org/content/10.1101...

and here from a Nature article: rdcu.be/bREbC

Jackie

[AussieNeil Partner Administrator]

Wow! Not only is this technology looking promising for being able to do a complete CLL genome scan, the second article from 2017 noted how it was already being used to quickly identify pathogens in blood in 10 hours and forecasting it would be possible to do this in about 6 hours by now. This could save many lives by cutting the current several days to do cultures to determine the best antibiotic to less than a working day. WOW!

Great to read that the technology can work to identify epigenetic modifications to the DNA too (how gene expression is silenced) as the understanding of that process is crucial in working out how we get such heterogeneous expression in CLL.

For those wanting an abridged description of the technology, DNA sequencing works by breaking up one long strand of DNA into lots of small segments, reading those segments and then guessing how the segments were originally joined. We can't currently read a full DNA strand in one go. It's like the only way of identifying an object is by taking a picture that is delivered as a 100,000 piece jigsaw, then having to reassemble the jigsaw pieces to identify the object. This technology is quickly reducing the number of jigsaw pieces so that the picture - the complete genome, can be reassembled quickly with less mistakes. That's why the time to get results is reducing from days to hours

Neil

[bhayes84 in reply to AussieNeil]

That’s interesting that they can get epigenetic information from an unwound segment of DNA.

[Smakwater]

The dynamic in research and medical technological advances is astounding!

Where is it going? Very Cool.

JM