Win a free MiSeqV3 600 cycle run: the Core Genomics Christmas Competition

Last month I posted a logical puzzle to see if people knew how much different next-gen sequencing applications cost? The repsonses have been varied!

Now Illumina have very kindly donated a MiSeq run and 250 iCredits as the prize for a festive competition. You can win a MiSeq 600 cycle run, which I'll put on one of the MiSeq's in my lab and deliver the data via BaseSpace, where you'll be able to use your free iCredits to analyse data using the BaseSpace apps.

Will anyone get his or her genome sequenced at AGBT this year?

Given HiSeq 2500 and Ion Proton it is entirely possible for someone to sequence their genome in the Illumina or Life-Tech booth’s at AGBT, so will anyone attempt it?

"A bridge too far" for consumer genomics?

It’s amazing what is being done with DNA sequencing. Cancer genetics and personalised medicine make headlines, consumer genomics has been in the news and Genomics England are going to sequence 100,000 NHS patients. But all that glitters is not gold!

23andMe vs Lisa Casey

Updated after reading Dale Yazuki's blog pointing to this post by Lukas Hartmann, which I've sumarised next to Shaheen Pasha's below.

Poor old 23andMe; first the FDA and now Lisa Casey, can they survive? And what would their failure mean for personal genomics?

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!

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We recently had out Institute symposium; lots of talks about the science going on in the building, mostly unpublished work and most of it very exciting.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.

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?

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:

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.

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!