Tuesday 23 December 2014

Monday 22 December 2014

Extracting cell-free DNA from plasma

Two major problems are encountered by researchers wanting to analyse circulating tumour DNA; contamination by gDNA from white blood cells; and the relatively low amount of circulating DNA. Because of this the protocols used for blood collection and circulating DNA extraction are critical. This post describes some of the challenges in more detail and reviews some of the kits available.

Friday 19 December 2014

Authorship and acknowledgment of core facility work

I've been lucky enough to work in an Institute that views its core facilities as a cornerstone of the scientific output, and we get acknowledged for most of the work we do. Other core facilities are not so lucky; and even here sometimes people simply forget to acknowledge everyone they should have in the rush to get their paper submitted.

Now the journal BioTechniques has introduced a new editorial policy that will require authors to answer the question "if they worked with a core laboratory", and if so make sure this is acknowledged in the final manuscript. I hope other journals will take a similar decision. All core labs are funded, completely, or in some part, by grant income and are effectively subsidised. This is the main reason core labs are usually cheaper than commercial providers. This funding is not wasted by the host institution as the cores (should) offer a more flexible and bespoke service.

Tuesday 9 December 2014

Top 100 papers of 2014: courtesy of Altmetric

Congratulations to Marc Tischkowitz and colleagues for getting into Altmetrics Top 100 papers of the year. Their NEJM paper on increase risk of breast cancer in loss-of-function PALB2 carriers was number 87 and one of two papers from the University of Cambridge.

The Altmetric Top 100 is heavily influenced by the media coverage of "newsworthy" publications and it is perhaps not surprising that the Number1 spot is taken by Facebook's rather controversial "emotional contagion" paper (covered by Retraction Watch).
No surprise that medical and biological sciences top the list with around 60% of papers in these categories. I was pleased to see that 80% of articles included an author from the UK.

Monday 8 December 2014

Genomes, exomes or amplicones: what's best for the clinic?

Clinical sequencing is looming and recently I've heard more, and better, arguments for using whole genomes. These have mainly focused on the quality of PCR-free genomes, which have uniform coverage and few regions of missing or very low coverage. Compared to the PCR and hybridisation-capture artefact's in exomes, or the focus on a biased set of genes a genome can sound very convincing (especially if you ignore the analysis/storage issues). Until recently the cost has still been too high, but Illumina recently released PCR-free on X Ten reducing the cost substantially. However there are so many different arguments that it is difficult to determine if we can perform a one-size-fits-all sequencing experiment.
Comparison of Illumina PCR-free to PCR+ kits

Recently I started talking to people who use terms like analytic validity, clinical validity and clinical utility - these meant something to me, but what they meant for genome sequencing assays, exomes and amplicomes I was not so sure so I thought I'd find out.

Tuesday 2 December 2014

XNA ink in your Sharpie: an indelible marker for genomics

New research at the LMB (across the road from the Institute I work in) has demonstrated how alternate "genetic polymers" can be used in place of DNA and RNA: Synthetic Genetic Polymers Capable of Heredity and Evolution. XNAs [xeno-nucleic acids] use nucleotide analgoues, and the trick has been to get these to work in a biological system by engineering polymerases and other enzymes.

XNA structure from Pinheiro et al 2014