Friday, 29 January 2016

FlowCNV-seq: an almost novel metthod for single-cell copy number analysis

I recently presented at the Festival of Genomics on a proof-of-concept experiment we ran in my lab to generate single-cell copy number profiles. The experimental work was done in 2014 and we're now looking to port the method over to Fluidigm's C1 chips, possibly using the smallest IFCs to capture nuclei rather than cells. Although there are some wonderful systems out there for single-cell analysis most labs already have flow cytometry facilities conveniently to hand, and sorting cells in to plates is reasonably simple – even into 384 well plates. We showed that coupling flow sorting to low-volume library-prep, using Rubicon's PicoPlex kit, produced good results at reasonable cost.


Monday, 18 January 2016

(almost) everything you wanted to know about @illumina HiSeq 4000...and some stuff you didn't

The HiSeq 4000 was Illumina's way of making the patterned flowcell technology available to non X Ten customers, and opening up patterned flowcells to applications other than Human genomes. The list of supported library preps is still relatively small: TruSeq Nano, TruSeq PCR Free, Nextera rapid capture, Truseq mRNA stranded, Truseq total RNA stranded, TruSeq RNA access - basically TruSeq! However customers are running many unsupported library types after a bit of internal testing. For some applications HiSeq 2500 is likely to remain the platform of choice - particularly for the libraries which are HiSeq 4000's "classes of evil".


BTW: this is a big post - sorry! I'm going to follow up with a post about the "ExAmp" duplicates and how they may be a problem for some applications. And I'll also follow up as we get some real data comparisons between HiSeq 4000 and 2500v4

Win a Mini (and a Mini-seq too)

Illumina are offering the chance to win a Mini in a competition to drive interest in their MiniSeq, the competition grand prize winner gets a MiniSeq and an Illumina-branded Mini Cooper (probably pumpkin, possibly black-and-white).
The competition is a grant program; to enter tell Illumina in 500 words or less how you would use MiniSeq in your own research. Abstracts will be judged by a team of Illumina scientists (not Core-Genomics) and will be winners will be judged on scientific merit, innovation, and fit with the MiniSeq system.

Entry by March 31, 2016. Winners will be announced at the American Association for Cancer Research 2016 meeting in New Orleans.

PS: Please do tag my posts on Twitter so I'm in with a chance to win an iPad mini it the bi-weekly social media contest Illumina are also running!

Saturday, 16 January 2016

What does "cure" mean?

President Obama's "moon shot" to get a cure for cancer has received a lot of coverage, both positive and negative. GenomeWeb pulled together some of this in a Scan article earlier this week: "Is a Cure Even Possible?". This reported on coverage from The New York Times, Scientific American, and others including blogger Whizbang.  The NYT coverage included calls for more funding of cancer research by the US government, and this was also echoed in Whizbangs post - both were making the case for funding basic biology.


Thursday, 14 January 2016

Scientists from David Zhang's group in the NABlab at Rice University, Texas, and nanoString technologies had their work featured on the front cover of Decembers Nature Methods: Continuously tunable nucleic acid hybridization probes. The paper describes their work with X-probes and/or ToeHold probes to tune the performance of oligos in a hybridisation reaction, and demonstrate this with almost perfect yield across 31 probes designed to Staphylococcus aureus in a Human genomic DNA background.


Wednesday, 13 January 2016

What do Fludigms problems with the C1 IFCs mean for users?

Fluidigm President and CEO Gajus Worthington sent a message to C1 users today that reported problems with their C1 IFCs, particularly those for medium-size cells (10–17┬Ám), The issue is an unacceptably high level of doublets i.e. two-cells in a capture site rather than one. The medium size C1 96 IFC has approximately 30% doublets with a standard deviation of 10%; the HT IFC has approximately 44% doublets with a standard deviation of 23%; and even the small and large size 96 IFCs (not the focus of the message to customers) have approximately 10% doublets with a standard deviation of 4%...single-cell this is not.

Fluidigm will have had a tough Christmas deciding how to handle this. Whilst painful I'm glad they've contacted users and put out this message. A white paper is available that describes what Fluidigm have done to investigate the problems, and it has recommendations for doublet detection: Doublet Rate and Detection on the C1 IFCs. They have already said that development of new IFCs designed to reduce the incidence of doublets should be available by spring, i.e. April.
 

Monday, 11 January 2016

Meet the newest members of the family: MiniSeq & Project Firefly

Jay was busy at JP Morgan. GenomeWeb have excellent coverage of all the big announcements; for me the most interesting is the information about Grail - the new liquid biopsy screening company and I covered that earlier today. In this post I thought I'd give my first impressions of the new sequencer - the MiniSeq, and some


Illumina locking down NIPT tech while launching ctDNA company

Illumina’s been busy in the cell-free DNA world, on the eve of JP Morgan Jay Flatley announced a new company, Grail, to screen cell free DNA for cancer. And at the end of last week Illumina ramped up litigation against companies using cfDNA for NIPT testing.

Thursday, 31 December 2015

Christmas in the Core and a New Years perspective on NGS genomics

Christmas came a little early to my lab with the delivery of two new HiSeq 4000 instruments. It would have been nice if these had come gift wrapped as it is the Christmas season, but alas no. Perhaps next year Illumina can get a little more into the Christmas spirit? I recently contributed to a 2015 review by GenomeWeb and thought I'd give a more in depth view of 2015, and what might be coming in 2016, from my perspective.

Wednesday, 16 December 2015

Can't find your primers? Don't bother looking!

PCR primers have become so cheap we had a discussion in the lab today about whether we should simply reorder, rather than try to find some old ones that weren't where we thought they were! This rather glib suggestion made me think about how long I should look before giving up and simply reordering.

At around £0.10 to £0.25 pence per base a pair of PCR primers will set you back £5-10. A post-doc salary is about £16 per hour based on the average salary of about £30,000 per year. So if you can't find your primers in about twenty minutes, give up, place a new order and wait till they arrive.