Saturday, 13 February 2016

AGBT16 it's the final countdown!

Saturday, February 13, 2016 14:45
Def Leppard are playing "Pour some sugar on me" while we wait for Nick Loman to walk on stage - not sure if this was intentional.



Nick Loman, University of Birmingham “Real-time genome sequencing in the field”. Four years since Clive's 2012 AGBT talk where ONT launched the MinION, Nik's work is now being retweeted by Bill Gates and he's changed his talk tile to reference this. Nik started by referring us to the gap in the data presented in Pardis Sabeti's Nature paper showing gaps in the data delivery in the Ebola outbreak.

Nik wanted to set the record straight on the size on the MinION: it is not the length of an iPhone (Loman et al. Bioinformatics 2014), or an office stapler (Watson et al bioRxiv 2015), and recently reviewers asked Nik to remove a reference to a chocolate bar.

More seriously Niks presenting data on the work with Josh Quick, Miles Carroll (European Mobile Labs) on the sequencing of the 2014 Ebola outbreak with Oxford Nanopore's MinION sequencer. You can read more about this in many places, BioMedCentral, Nature, The Vergesmokeandumami...oops that's Nicks food blog. Most Ebola cases were sequenced within 48 hours of sample receipt. Data shared on ebola.nextstrain.org "the model for how we should do this in the future". He finishing up talking about BentoBIO box
and handheld PCR, isothermal amplification, etc.

The AGBTome: the first genome has now been sequenced at AGBT: 85x coverage E.coli genome! (did the hotel know this going on in Nik's room)

This work has been a big collaboration, lots and lots of people involved including ONT (big help with reagents and advice), and also with Jared Simpson who developed tools to use the raw MinION signal to call variants with high sepcitifity and sensitivity.

Susan Rosenberg, Baylor College of Medicine “Freeze-frame synthetic proteins trap genome damage intermediates in living cells” asked people not to blog or Tweet.

Shawn Levy
Shawn Levy, HudsonAlpha Institute for Biotechnology  “Unique run conditions allow multiplexed phased genomes on the HiSeq X to reveal high-resolution copy number changes and high-quality variant calling” - the longest title at AGBT, but at least it's the same as in the abstract book!

It is only a decade since Solexa sequenced PhiX...and now we've got "10X on X Ten". Shawn's lab got the GemCode platform in May/June and have been working with it ever since. The V1 10X chemistry did not work on the X Ten platform, and Shawn was reluctant to answer a questions from Mike Quail (WTSI) about how to do this. GemCode requires both a standard TruSeq genome and a 10X genome to be run. The Chromium chemistry gets rid of the need for the TruSeq library. Shawn recommended aiming for 120Gb of sequence, 425 million reads, to get the best from the protocol. This is working well in their hands and variant calling concordance from a single nanogram library compared to a standard 1ug input is 0.999, only 0.7% of the genome is missing due to lack of coverage, showing that the 1ng libraries are very diverse. All in all a pretty good experience so far at Hudson Alpha.

Shawn spent some time talking about what they saw that was new information compared to what could be seen with a standard library prep. He showed a lovely example of many mis-sense mutations phased in a healthy individual confirming only one allele was faulty. Also showed 10X sequencing of non-Human genomes - the clouded leopard genome.

That's almost it...there are three more talks but I'm going to Tweet those instead. See you at the party.

2 comments:

  1. You always focus on the point of great interest. Well done.

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