What 5G mobile networks portends for the future of personal genomics

ok I saw this a while back (a month ago, yes I have been busy) http://www.engadget.com/2014/10/14/samsung-5g-network-tests-oh-god-the-speed/

I am already very impressed with 4G (LTE) speeds but with 5G you can possibly achieve 150 mb/s to 940 mb/s which is mind blowing ...

Considering that you could then possibly upload via your mobile devices, your own 100 Gb bam file in about 10 seconds (sorry I wasn't thinking how much faster a youtube video would stream). Now Google is saying that they can store your genome (actually they meant your 30x WGS bam file) for $25 a year. But with 5G speeds, why would I even bother with that?

Heck, maybe in the future with an USB OTG cable connected to Oxford Nanopore's MinION your android phone will be able to sequence and upload in realtime your DNA obtained from a buccal swab. The cloud will have the fastq reads aligned and call variants instantaneously and download the 100 Gb bam to your microsd card.

Possible applications:

1. Maybe in the future other than asking if you have a drug allergy, pharmacists will request to 'scan' your DNA for the most efficient drug. 
2. another possible application might be having your DNA be your own personal identity card, 
3. more routine sequencing of the human microbiome to monitor your health in relation to the gut microflora or other sites.

I am keen to find out what you think you can do if you could carry your whole genome sequencing with you and upload via mobile networks. Drop in your comments please!

Oxford Nanopore megaton announcement: “Why do you need a machine?” – exclusive interview for this blog!

http://pathogenomics.bham.ac.uk/blog/2012/02/oxford-nanopore-megaton-announcement-why-do-you-need-a-machine-exclusive-interview-for-this-blog/

woke up this morning to see a whole bunch of excited tweets on Oxford Nanopore and I can totally understand why. This is the real democratization of DNA sequencing. Move over benchtop / desktop sequencers for 'laptop sequencers'!

Hmmm or a cluster of sequencers, on your compute cluster ... !

Using USB powered sequencers, and a pipette to put in the dsDNA and you might have your sequence read to FASTQ directly to your laptop. 

No known limit to read length. 

4% seq error (the good thing is that the form of error is known and therefore correctable)

Do read the url above for more info, here's the excerpted executive summary for the impatient

Executive Summary

• Nanopore have announced a strand sequencing method, made possible by a heavily modified biological nanopore and an industrially-fabricated polymer
• DNA passes through the nanopore and tri-nucleotides in contact with the pore are detected through electrochemistry
• Demonstrated 2x50kb sense & anti-sense of same molecules (lambda phage) – no theoretical read length limit
• Can sequence direct from blood without need for sample preparation
• Two products announced:
  • MinIon – USB disposable sequencer for ~ $900 has 512 nanopores – target 150mb/hour
  • MinIon can run at 120-1000 bases/minute per pore for up to 6 hours
  • GridIon – two versions of rack-mountable sequencer with 2000 nanopores (2nd half 2012), 8000 nanopores (2013)
  • GridIons can be racked in parallel, 20 could do a whole human genome in 15 minutes
  • Each GridIon can do "tens of gigabases" over 24 hours
• Both machines commercially available 2nd half 2012
• Sequencing can be paused, sample recovered, replaced, started again
• Accuracy is 96%, errors are deletions, error profile will improve through software

Check out Forbes interview with 454 / PGM inventor Jon Rothberg

"Rothberg noted that Ion Torrent’s new machine, the Proton, the company showed three completed human genomes yesterday at AGBT. More importantly, he had the machine – not a mock-up or a design – on the stage. “That’s where you need to be to ship mid-year,” he writes."


Over at Genomes Unzipped 
Oxford Nanopore CTO Clive Brown related how sequencing library prep is as simple as diluting rabbit's blood with water. Now that is impressive!




This post is getting too long because I keep updating it. 
Over at the BioITWorld, there's an interview with Clive Brown which cites other interesting info. 
First of which is the opening paragraph which is amusing in the light of ONT's rivals comments
"Clive Brown, vice president of development and informatics for Oxford Nanopore Technologies (ONT), a.k.a “the most honest guy in all of next-gen sequencing,” as dubbed by The Genome Center's David Dooling, is hoping to catch lightning in a bottle again. "


Oxford Nanopore has not yet revealed details of its future platform, but in early 2009, published a lovely paper in Nature Nanotechnology showing that its alpha-hemolysin nanopores can discriminate between the four bases of DNA (not to mention a fifth, methyl C)




Directly get methylation information from your sequencing sans complicated sample prep? That has to be another selling point. 


Not sure whether Nanopore is truly vaporware. However, gauging by the excitement over the blogosphere and the hit rates for the first to blog about it. I think Nanopore is upping the ante for the next IT sequencer. 
maybe we can only survive 2 more AGBT like this and AGBT might fizzle out as new sequencing technologies fade as our computation advances trails behind the ability to generate more data. 
Maybe you will see scientists start attending Big Data tech conferences or AGBT's  main draw will  fancy new software to assemble, align and make sense out of all the data being generated ... 




This picture tells quite a story (Wordle constructed from 3,386 tweets and retweets tagged #AGBT with @s removed).
No prizes for guessing the winner ...