Illumina's new sequencers - my initial thoughts

Illumina continue to push hard on making DNA sequencing cheaper and easier to access for everyone. The announcements at last night's JP Morgan included a smaller X Ten, HiSeq 3000/4000 and NextSeq 550. I'm not going into much detail about the instruments, you can get the specs on Illumina's website, but I will talk about the impact the next step in Genome Analyser evolution.

Briefly the XTen is joined by the X Five System, half the price and only 9,000 genomes a year. The NextSeq 550 allows labs to also scan Illumina microarrays (remember those), but the focus is clearly cytogenetics and PGD - the system is not capable of running HT12's for instance.

HiSeq 3000/4000: The latest update for HiSeq is another big step forward, and somewhat surprising as it comes only a year after the release of V4 chemistry on the 2500. The patterned flowcells are here. Interestingly there was no mention of upgrades from 2500 to 4000. The 4000 is the machine I'd be wanting in my lab and the specs are pretty exciting: 1.5Tb in three das on PE150bp, 5 billion clusters (the Ga was lucky to get 1M per lane when first released), and still with high quality and ≥ 75% bases above Q30. 12 Human Genomes or 180 Exomes or 250 RNA-seq per run - we'll be busy making libraries!

ctDNA: Illumina also presented their circulating tumour DNA R&D program with kits coming in 2015 something we'll be watching closely.

I'll post again in the next day or two once I've distilled my thoughts on the impact for labs like mine.

The not-so-rapid decreasing costs of genetic testing

There is a whole big noisy discussion going on around the regulation of NGS tests, which has been covered in some detail by GenomeWeb and other bloggers. My lab does not develop tests, but I have a real interest in seeing how NGS is being translated to the clinic and reading what's going on is very interesting indeed.

GATC: acknowledging the acknowledgment

Shortly after writing my post on Authorship and acknowledgement of core facility work I was pointed to the GATC Top publications of 2014. Here GATC list the papers where their sequencing (and other) services have been used and acknowledged.

Congratulations GATC: four Nature and one Cancer Cell papers in your 2014 Top 5 can't be bad!

Merry Christmas from CoreGenomics

Have a great Christmas break...hope to see you in 2015. James.

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.

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.

Book Review: Fred Sanger's biography

Fred Sanger - Double Nobel Laureate: A Biography.

Author: George G. Brownlee.

Publisher: Cambridge University Press (2014) ISBN: 9781107083349

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.

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.

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