Friday, 29 April 2016

SPRI alternatives for NGS

SPRI beads, generally in the form of AMPureXP beads, are almost ubiquitous in genomics applications such as library prep for NGS. The most popular thing I've ever written was a post on this blog four years ago: "How do SPRI beads work?" with almost 100,000 readers - people obviously want to understand how this wonderful technology can be used. They'd also like it to be cheaper as the Agencourt AMPureXP product (now Beckman) is somewhat expensive - so I've taken a look at some of the alternatives on the market, including DIY SPRI!

Thursday, 28 April 2016

The junior doctors explained to me

I met two dads last night, one a junior doctor picking his daughter up from the same Karate class my son; the other, a consultant, at the pub after a long day (covering for junior doctors). Both of them spoke about the junior doctors strike and some of what they said is mind boggling. How have we come to such a sorry state in the NHS? Are doctors simply overpaid since contracts were changed by Blair and co? Are the managers of the NHS just after balancing a budget with no thought for the impact their decisions might have on other departments? And does Jeremy Hunt deserve to have his name used as Cockney rhyming slang?

This is how the situation was explained to me:
  • A BMJ paper in September 2015 showed that patients are 10-15% more likely to die if they are admitted on a weekend. [This work has been criticised as flawed due to the complexities of comparing patients admitted on different days - you may actually be sicker at the weekend. But the paper has an errata as it turned out that one of the authors Bruce Keogh (medical director of NHS England) is "a long standing proponent of improving NHS services seven days a week" why the BMJ should have to "have requested that this be included in the authors’ conflict of interest statement" I don't know - seems obvious to include it to me.]
  • Because of this the government in England has decided that NHS services should be available seven days a week.
  • They have proposed a new contract for junior doctors that changes the hourly rate they get after 7pm and at the weekends, and they won't get annual pay increments, instead pay progression will be linked to training.
  • Junior doctors already work weekends.
  • Junior doctors say the new contract will not add new doctors to the system, but it will make them cheaper to pay at the weekend.
  • Both parties cannot come to an agreement so junior doctors have gone on strike.
How will pay change: The Financial Times has a nice graphic showing how the current pay structure compares to those proposed by the government or the BMA. And the BBC also have a graphic showing the junior doctors rates for unsocial hours, I used their numbers to try and see how different the positions are and it really did not seem to be worth striking over - I make the BMAs suggestion as cheaper that the governments!?!


The aim appears to be to get more doctors working at weekends, and it should make paying them at weekends cheaper than today so money will be saved. But the consultant I spoke to used a single example to show how much waste is happening in the NHS - and that fixing this would have far more impact than changing junior doctors rates of pay.

An example of NHS waste: The consultant described an elderly patient who needed a mental health referral before discharge, however the person who would do this was on holiday for a week, so the consultant's patient has to stay in hospital. This blocks the bed for 7 days at around £400 per night (that's the equivalent of The Goring in London, or The Waldorf Astoria in New York). If 10 patients are in the same situation then the bill for this persons one weeks holiday comes to £28,000 or equivalent to a junior doctors salary...and most people get six weeks holiday in the NHS.

The NHS does wonderful things for the UK but successive governments have seriously messed it up. My wife recently spent time in Addenbrookes and whilst she received adequate care the communication from doctors and nurses was abysmal, the food can not be described using any positive adjectives, and the accommodations are pretty terrible given the cost of the bed for the night. I'd love to sing the praises of the NHS but it does feel like big changes are needed...but I am not suggesting I can come up with any useful ideas!

Thursday, 21 April 2016

Fluidigm's single cell issues appear to be fixed..sort of

Fluidgm hosted a webinar this afternoon to describe the performance of the redesigned IFCs for medium-sized cells (10-17um), they've also released a whitepaper on their website describing their work. The redesigned medium-cell 96 IFCs have a >4-fold reduction in doublet rate at around 7%.

This is a significant improvement (and I've written up my notes from the webinar below)...but is this level of doublets low enough for the kind of experiments single-cell users might be planning?

Create your own user feedback survey

Monday, 11 April 2016

WGS versus Exome: what's best for cancer?

I've just started using Twitter polls and kicked things off with a couple asking followers whether they thought Cancer research (or diagnostics) is best investigated using whole genome sequencing, higher depth exomes, much higher depth amplicomes, or even long-reads. Please do take the poll and join in the conversation here or over at Twitter.

Here's a link to the cancer research poll, and here's one to the cancer diagnostics poll. Pass onto your collegaues. I'm going to follow up in a week with a post outlining my thoughts and particularly where long-reads might have a real impact in understnading structural-variation in cancer.