Pocket sized genone sequencing ?

Capt'n Midnight

When the human genome project started in 1990 it was estimated it would take 15 years and cost $3Bn at at time when the average Irish house price was just €65,000 (CSO)

Today you can sequence as little as a single strand of DNA with a reader you can fit in your pocket. GATTACA gets less far fetched every day.

http://www.bbc.com/news/health-42838821
https://arstechnica.com/science/2018/01/pocket-sized-dna-reader-used-to-scan-entire-human-genome-sequence/

Dingle_berry

Interesting times ahead! But what's underplayed in those articles is the bioinformatics required to translate the sequencing into meaningful data. And then the knowledge of how genome actually affects phenotype... is the general public ready for the ability to know wether they share genes with most other Heart attack / dementia sufferers?

Capt'n Midnight

Had the heel prick samples been kept and anonymised we could in theory done a mass screening to predict the prevalence of certain markers , and used the info to budget for future health spending.

But yes DNA is a bit like an ancient writing system that we have only partially deciphered.

Tree

I want to see the miniions stuck on to a phone and the informatics done there and then but I might be overestimating the capabilities of phones and the miniion's capability of being swung around beside your head making the odd call... oh no, uploaded data to the server while roaming is how much per kb??

josey_whale

Oxford nanopore are developing a system for a phone - The smidegION. This device has 256 channels/flow cell. Channel = pores. The minION has 512. The big advantage nanopore sequencing has over sequencing by synthesis methods such as Illumina sequencing is the read length. In that most recent paper they were able to get read lengths of up to 882kb - incredible! With these sorts of read lengths, you can accurately determine telomere repeat lengths and other regions with a lot of repeats. Another cool thing about this technology is the ability to directly sequence RNA without the need for RT.

The above said, an issue with Oxford Nanopore's technology, is that the pores are actually pore proteins (an engineered E. coli pore protein - CsgG). Although the minION software can predict the number of functional pores before a run is started, typically only 300 of these are functional. Also, they need to be stored at 2-8C and have a relatively short shelf life (2months). Another issue is the sequencing accuracy. It's in the order of 98-99% - very good, but for many applications not good enough. It will improve though.

The next generation sequencing -4th gen (if we call Oxford nanopore sequencing 3rd generation), will do away with biological pores altogether. It will be a solid state pore. There is some really cool research going on in this area. Theoretically, sequencing speeds could be in the order of 10^6 - 10^7 bases/second. Just think how scalable this could be. A further application of solid state nanopores will be the ability to sequence proteins.

Oh, and just to add - Don't forget that DNA is the ultimate information storage molecule. Nanopore sequencing is is exactly the kind of technology that will be required when DNA starts to be used for data storage.