Saturday 30 November 2013

How much does NGS cost: a logical puzzle

At our recent institute symposium I added an additional graphic to try and get people thinking about how much their sequencing costs.

Can you work it out: Below are six pairs of circles representing genome, methylome, RNA-seq (GX), ChIP-seq, Exomes and amplicons, size is proportional to cost and the two colours represent library preparation and sequencing.
  • Can you determine which application is which?
  • Which colour is library prep?
  • Which colour is sequencing?
  • How much do you think each application costs?

Answers in the form of comments or drop me an email. The results here surprised me, I thought people had a better idea of the actual costs but it turns out people have some pretty wild ideas!

Friday 29 November 2013

Genome-infographics: making sense of what we do

We recently had out Institute symposium; lots of talks about the science going on in the building, mostly unpublished work and most of it very exciting. I am always amazed at how lucky I am to be working in a place that uses genomics so widely, this year we had talks from many of out non-genomics groups that still included some work performed in my lab. Genomics is getting (almost) everywhere!

For the poster session this year I wanted to use infographics to create some nice visualisations of what we've done over the past seven years. I thought I'd share these and point you to the resources I used to create them.

Thursday 28 November 2013

Myriad: school bully, or just sticking up for themselves?

Can some explain Myriad's strategy, other than using bullying tactics to kill competition I don't get it? Is there any real prospect of the law siding with their point of view? I hope not. And since the US market has some pretty wonderful advertising (surely you all remember the PGM vs MiSeq ad series), surely Myriad will end up damaging their own reputation with consumers therefore shooting themselves in the foot?

Monday 25 November 2013

Sanger-seq is dead: If you only read one paper this month read this one...

Foundation Medicine published a wonderful paper in Nature Biotechnology last month. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing describes their approach to personalised cancer  genomics.

Foundation Medicines "Foundation 1" test allows NGS analysis of 287 genes from FFPE samples for SNPs, InDels, CNA's and fusions. They describe the design and testing of this panel along with results from over 2000 clinical samples, finding "clinically actionable alterations in 76% of tumours" 3x more than they say are found with current methods.

Is Sanger-seq is dead:

Thursday 21 November 2013

Nanopore sir? should be delivered in 2014 or perhaps 2030!

Many of the readers of this blog will have seen the announcements from Oxford Nanopore Technologies on their MinIon early access program. The people I talk to are almost universally excited; if a little sceptical about how quickly we’ll be getting rid of our HiSeq’s and Proton’s.

Wednesday 20 November 2013

RIP Fred Sanger

Fred Sanger died today aged 95. A sad day for science but one where we can remember the phenomenal impact his work has had on us all. Of course being a genomics lab makes his work all the more important, but almost everything done in biology makes use of his advances in the form of sequence data.

We don't use Sanger sequencing as much as before, nearly all the biology I'm involved in uses next-generation sequencing. But I am sure Shankar Balasubramanian, David Klenerman, Johnathan Rothberg and George Church will all be raising their glasses to one of modern sciences greats.

The Cambridge News and The Telegraph both have very good obituaries.

Goodbye Fred. I wish I'd met him!

Monday 18 November 2013

Can it hold a pipette?

Don't we all get tired of being in the lab and wish we could work from home sometimes? Office workers do it fine and now they have a robot to help them keep in touch with colleagues in the office.

I'm not exactly sure how we might adapt this to hold a pipette, and I'm not sure but I don't know of many labs in bungalows!

96 ChIPs? That’ll fit on one of Illumina's new patterned flowcells

ENCODE was a mammoth endeavor, and one that is helping to better shape our understanding of biology, but the project required a large multi-national collaboration to generate the 1000’s of ChIP-seq and RNA-seq libraries. Last week Duncan Odom’s research group at the Cambridge Institute published an automated ChIP-seq pipeline in Genome Biology capable of generating 96 ChIP-seq libraries with just 2 hours hands-on time making the lab-work for projects of ENCODE scale possible in just a few weeks. With all the samples on a new higher-density patterned flowcell perhaps?

Friday 15 November 2013

How to access BaseSpace forums

If you are using Illumina's BaseSpace then you probably run into some of the same frustrations as myself and other users, however Illumina do provide a feedback mechanism and a forum to suggest ideas for development. Finding this can be a bit difficult so in order to remind myself next time I want to find it, and to help others who may be looking, I wrote this post.

Thursday 14 November 2013

$100million for the Broad: what have they done for genomics?

When the Prime Minister announced £100M and the creation of Genome England we thought we had made the big time here in the UK. But compare that to the Broad's latest gift of $100M and our national effort suddenly doesn't look so big!

Wednesday 13 November 2013

Dr Evil's exome seqeuncing services

Sequencing service providers are popping up everywhere and offering some great deals on genomes, exomes and RNA-seq. How can this sequencing be so cheap I hear some of my users saying? The costs are usually dependent on a certain volume of work and are likely to bring in lots of the same sort of sequencing at once, while the promotion is on. Running RNA-seq in 96-well plates and across multiple short-read flowcells is very efficient so big savings can be made this way and providers are keen to pass those savings onto you to get your business and hopefully keep it. I think we’ve almost reached the point where NGS reads are a commodity and people just want them as fast and cheaply as possible, just like Sanger sequencing.

Thinking about this made an idea pop into my head, not one I’m going to pursue but one I thought readers of this blog would like to hear about.

Welcome to Dr Evil’s Sequencing Centre:

Tuesday 12 November 2013

PubMed commons: how will we use it?

PubMed commons is hoping to create somewhere for researchers to "share their opinions about scientific publications", it is going to be for "open and constructive criticism and discussion of scientific issues" and will "depend on the scientific quality of the interchange". Your comments are made available under a CC license so everyone can reuse them and comments are moderated (I already saw one that had been removed).

Friday 8 November 2013

Personal Genome Project UK and Dr Evil’s frame-up

-->George Church started something great back in 2005, now Stephan Beck at the UCL Cancer Centre has kicked off the UK’s own Personal Genome Project. The idea has always been a simple one, get data from willing participants, make genome sequencing free and make the data available on a free-to-access model. The PGP has always aimed to be clear that there is little in direct benefit to participants; except of course the warm and fuzzy feeling that only your genome being sequenced can give you!

Dr Evil is back: The PGP website lists some of the benefits to science, I won’t well on those here. They also talk about some of the risks and one in particular caught my attention; that data might allow someone to “make synthetic DNA corresponding to the participant and plant it at a crime scene”.