Wednesday, 24 April 2013

The blogs I read & M. leprae's magic tricks with stem cells

I have recently added several more blogs to the list on the side of this page, these are blogs I enjoy and I hope you find the posts on them as interesting as I do. Choosing to follow a blog always seems a bit of a big step. It adds to the burden of interesting things to read, as if we didn't have enough coming out of science journals, GenomeWeb and other sites. I try not to add anything I don't want to read long term as I feel terrible taking someone off my list, it feels like a personal attack!

Friday, 19 April 2013

A $1000 genome for a $400,000 drug

The NGS community has been talking about the $1000 genome as a holy grail (expect it in the second half of 2014), but on the way to this the exome is looking like it will become a cornerstone of modern medical research mainly because of the ease and costs of generating the data. The NIH launched the Undiagnosed Diseases Program in 2008 and in the first three years had sequenced around 250 exomes from case book of 1800 patients. One of the programs aims was to reduce the time taken to accurately diagnose patients, which for 15% of people was taking more than 5 years. The program attracted funding of $3.5 million a year (2010-2012) and has had some big successes. Read The NIH Undiagnosed Diseases Program: Lessons Learned to find out more.

Wednesday, 17 April 2013

The 8 rules of cake club

  • 1st RULE: Everyone votes at cake club.
  • 2nd RULE: EVERYONE votes at cake club.
  • 3rd RULE: If someone says "burnt" the cake is over.
  • 4th RULE: Only one person can bake.
  • 5th RULE: Only one cake at a time.
  • 6th RULE: No shop bought, no spouse-made.
  • 7th RULE: Cake will be eaten until it is gone.
  • 8th RULE: If this is your first time at cake club, you HAVE to bake.

Monday, 15 April 2013

MiSeq (and 2500) owners better read this and beware

Update 25th April: Illumina have released a support bulletin "Best Practices for High Sensitivity Applications: Minimizing Sample Carryover", this is accessible through Illumina's website, or SEQanswers. You'll need an Illumina login!

Illumina say that sample carryover is more likely to have an effect on very low detection threshold applications. Internal testing found sample carryover is typically below 0.1%, representing 1 read in 1000. Keep doing your maintenance washes (water and Tween) and do not use other wash additives, such as bleach, Triton or other decontamination solutions. 

The post as it was...
 A rather hot topic popped up on SEQanswers a few days ago. A new member Harlon, posted about seeing library contamination and carry-over between MiSeq runs; i.e. you get reads from the last run in the current one! So far the post has had almost 700 views and 13 replies. At least two are confirmations that this is being seen in other labs.

Are barcodes broken?

Saturday, 13 April 2013

2D RNA-seq rocks!

RNA-seq is getting very cool over in Sweden's SciLifeLab. A recent press release announces that Joakim Lundeberg (Royal Institute of Technology) Jonas Frisén and Patrik Ståhl (Karolinska Institutet) were awarded £1.8M from the Knut and Alice Wallenberg Foundation to study Brain biology. They have developed a method of 2-dimensional gene expression, 2D RNA-seq and will use this to comprehensively map gene expression in the brain. They also aim to compare normal and diseased brains, including cancer, autism and schizophrenia.

Thursday, 11 April 2013

ENCODE's RNA-seq recommendations need revising

One of the great things about ENCODE was the amount of effort put into standardising how different groups did their experiments. As any core manager knows a good SOP is a huge step to high-quality data. The ENCODE consortium put together guidelines for ChIP, RNA and RIP. Those guidelines, published almost a year ago, are due for revision in a month or so. I'm looking forward to the revised document as the current recommendations have some serious problems from my personal experience.

Sunday, 7 April 2013

ctExome-seq: Circulating tumour exomes as a non-invasive method to track tumour evolution during treatment

Monitoring of cancer patients is an important part of their treatment and this is traditionally done with tests like Computed Tomography imaging (CT) or biomarker analysis. NGS of cancer amplicons, exomes and/or genomes is being discussed as a realistic addition, and possibly an alternative, to these traditional methods. A major hurdle to their use is the fact that analysis of cancers can be hugely complicated by tumour heterogeneity and that serial biopsy of patients to obtain material for sequencing is not a realistic option for many patients. Although the analysis of circulating tumour cells has received a lot of interest, collecting the cells is no easy task (there have been some great papers that show what might be possible from CTC’s, the MALBAC method published in Science is a current favourite of mine). Nitzan Rosenfelds group at the Cambridge Institute has been pioneering the use of circulating tumour DNA (ctDNA) sequencing as a more amenable method to understand cancer genomics.

Next-Gen Sequencing pg’s of DNA with Thruplex (and other methods)

Sequencing from small amounts of nucleic acid is opening up new areas of research. Whilst microarray analysis of single cells has been performed in the past analysing the genome from such a small amount of DNA has been an almost impossible task. Equally, analysis of fragmented DNA in FFPE sections has proven to be technically challenging.

Friday, 5 April 2013

eBay as a way to equip your lab...

We have some old lab equipment we are getting rid of much of it will be recycled into other University departments. Some will be sold to equipment resellers like Biagen, Alliance Analytical, and Harlow Scientific. Some of it may even end up in the skip. But there may be one other place to advertise.

I took a look at what lab equipment was available and was quite surprised. My personal favourites were the Affy system, Robo Cycler PCR machine and the 377 DNA Sequencer.

I'd like to think you could equip a reasonable lab without leaving the comfort of your armchair. Imagine having this lot in your garage.

Monday, 1 April 2013

Finally a nanopore sequencer that works

Today I was given an exclusive preview from the newest nanopore sequencing company on the planet, Norfolk Nanopore Technology. The new "Polonopore"technology has been incubating in the Norwich Research Park BioIncubator under the same roof as TGAC.

NNT's brand spanking new nanopore sequencer could mean the end for the HiSeq, MiSeq, Proton and PGM platforms and paves the way for $100 personal genomes. NNT are suggesting very high yields from long-reads using Polonopore technology. $100 for 100x coverage of 100 genomes in 100 hours.