Tuesday, 6 October 2015

X Ten: now available for non-Human

Finally. Today Illumina announced that X Ten users can perform whole-genome sequencing of non-human species. Does this mean exomes and RNA-seq are on their way to X Ten? Or that an X One is going to be announced at JP Morgan? I might just hold off on buying that shiny new HiSeq 4000 until this is a bit clearer.

For small to medium labs the X Ten and even X Five were the stuff of dreams and nightmares. Dreams of what would be possible with this technology; nightmares of what might happen to smaller labs.

The dreams turned out to be true and the nightmares have pretty much gone away. But the rapid developments from Illumina continue to be difficult to keep up with. I only wrote about the performance of HiSeq 2500 V4 chemistry a little over a year ago, and it looks like we'll ditch it in favour of HiSeq 4000 in 2016.

The link on Illumina's webpage does not appear to be live just yet but I'm sure we'll hear more in the next couple of days.

PS: If your Wheat, Horse, Whale, etc, etc, etc genome sequencing grant just got approved you can look forward to a nice slush fund. Time to buy that Apple watch maybe?

Friday, 2 October 2015

Pub-Bed: beds, not papers

Would you stay at the home of another academic you had some loose connection with? Could the Airbnb model be successfully applied to help find accommodation for scientists travelling to meetings, visiting another lab, or even for longer sabbatical stays? I'm not sure but Pub-Bed was born from an idea I cooked up on the train.

Thursday, 1 October 2015

The new Pacific Biosciences sequencer

PacBio announced a baby RSII yesterday, which should be in the shops just in time for Christmas! The Sequel System (sounds like SequalPrep from Thermo for PCR cleanup) sounds like a big advance on the enormous RSII. Most aspects of the sequencing work flow are unchanged. Sequel has been developed as part of the collaboration with Roche to develop a diagnostics instrument, milestone payments of $20-40M are expected on the back of this.
  • $350,000 for Sequel (versus $1,000,000 for RSII)
  • Seven times more reads than RSII
  • 1/3rd the size and weight (so only 2000 or so MinIONs will fit inside)
  • New SMRT cells with 1,000,000 ZMWs compared to RSII's 150,000

Tuesday, 29 September 2015

Do you have a HiSeq 2500 V4 to sell

My lab is looking to put an additional HiSeq 2500 v4 in place, Illumina do not have any (refurbs) to sell in the US or Europe so I thought I'd post here to see if any Core Genomics readers have an instrument they are looking to retire? If we can offer you more than Illumina's trade-in on a HiSeq 4000 then we might be able to come to some arrangement!

Drop me an email at James.Hadfield@cruk.cam.ac.uk if you might be able to help.

Friday, 25 September 2015

Plagiarism alert via Twitter

I built several TwitterBots last year to scrape papers on PubMed (thanks again to Casey), these have turned out to be really useful in alerting me to new work but last night I got a very interesting Tweet from @MattiasAine...

Wednesday, 23 September 2015

Rubicon Genomics webinar on making cfDNA/ctDNA NGS libraries

Rubicon Genomics have a webinar on Creating Cell-free DNA Libraries with ThruPLEX Plasma-seq that was broadcast on September 17th 2015. The new PlasmaSeq kit has a very simple, 3-step, 15 minutes hands on time, single-tube workflow.

Dr. Kamran Shazand, Rubicon Genomics' Director of Applications presented an intro to cell-free DNA - generally 170bp fragmented DNA, which is the result of degradation by apoptocic enzymes, and that can appear in dimeric and trimeric nucleosomal fragments. Rubicon's earlier chemistry ThruPLEX was use in 2012/12 to sequence foetal and tumour genomes and it has a recommended input of 1-30ng of DNA.

The new PlasmaSeq kit seems to make very nice libraries. Internal data from Rubicon showed better performance against NEBnext and KAPA Hyper, with high diversity, low PCR duplication rates and good GC coverage. Most interestingly Rubicon have built a target capture pipeline using their PlasmaSeq kits, Agilent SureSelect and IDT blockers allowing exome sequencing from as little as 1ng of input DNA.

Methods: optimised DNA repair and ligation of stem-loop adapters, PCR to extend, cleave and amplify the library. You should end up with a major peak at 310bp for cfDNA libraries.

Rubicon also talked about their work looking into how molecular indexes night be added to allow removal of PCR duplicates to PlasmaSeq - -send them your comments if you are interested.

Disclosure: I am a user of Rubicon library prep technology; but also Illumina, NEB, Enzymatics, and many others too! I am an author on the ctDNA paper from 2012 mentioned above and in their webinar. I am on the SAB of Rubicon.

Research Professional: making finding funding easier

I'm incredibly lucky because I don't usually need to write grants. My lab is core funded by CRUK to provide genomics services to the CRUK- Cambridge Institute. However I do like to keep an eye out for opportunities to bring funding in for specific projects.

Our very good grants team pointed me to a tool that the University subscribes to *Research Professional. Once logged in I can easily search for new funding opportunities, if you've never used it it could become one of your favourite websites.

Research Professional began as a (print) “newspaper for the research world" in 1994, and moved to the web in 2001. It make accessible the opportunities and information on research grants to registered users and may institutions have purchased access. If your host Institute does subscribe then you should certainly take a look! You can search very easily and follow links directly to funders websites. The site generally provides a good summary of funding criteria so you can quickly weed out opportunities that you will not be eligible for.

Monday, 21 September 2015

Better ChIP, requires better antibodies

ChIP-seq can only really work if you have a good antibody for the protein of interest. Any non-specific binding is going to add noise to your data making motif finding, differential binding analysis difficult or even impossible. Back in 2008 Mathias UhlĂ©n's group at the Royal Institute of Technology, Sweden, published a study that showed how less than 50% of antibodies tested were specific to the target. 

Wednesday, 9 September 2015

#GenSci15 plenary session and wrap up

Sorry about the accidental posting...here's the final version.

Innes Barroso, Head of Human Genetics at Sanger Institute "Genomics and Metabolic Disease – what have we learned so far"

Type 2 diabetes, many patients controlled by table some on insulin, it is a very complex disorder, both genetic and environmental effects (particularly obesity, diet, exercise). Incomplete understanding of Type2 diabetes genetics, extended families are hard to obtain due to generally late onset. Progress has been slow, early studies failed to find robust loci that replicated across studies. However as power of GWAS studies improved six loci were found outside previously suspected candidate genes, but with small effect. Analysis of extremes can be very powerful i.e. young, lean patients vs old obese controls (similar approach being pursued in smoking with some success). Development of genotype imputation and meta-analysis had big impact on how GWAS could impact Type2 diabetes genetics. But still lots of "hidden heritability", drove development of custom GT chips e.g. Metabochip and UK Biobank Axiom array.

#GenSci15 day3 clinical genomics session

Andrew Beggs is chairing the clinical genomics session – this is why I am here, cool stuff!

Interesting that the Tolstoy quote from Pippa Thomson's talk (see below) "Happy families are all alike; every unhappy family is unhappy in its own way" came up, as it could be argued that the Anna Karenina principle probably applies to the clinical use of genomics right now: a deficiency in any one of a number of factors dooms it to failure. Clinical genomics can only have a successful impact if every possible deficiency in the study has been avoided i.e. clinical and family history, quality of exome coverage, issues with alignment etc, etc, etc,