Applications & Bottlenecks In Next Generation Sequencing

After months of preparation and the occasional sleepless night, November 5th arrived.  It wasn’t only Bonfire Night, but also the beginning of a two-day conference, focusing on NGS in clinical genetics laboratories.  Organised by my colleagues and friends from biotexcel and myself, it was held in the Manchester Conference Centre, in, naturally enough, Manchester, UK.

In order to break the ice, I had decided to deviate from the title of my opening presentation

and get the delegates to talk to their neighbours, explaining what they hoped to get out of the conference and writing this on a sheet of flip-chart paper, passing along each row.  This provoked a hubbub of conversation – which was what I wanted!  After this self-imposed interruption, I introduced the basics of genome-wide association studies (GWAS) and explained how NGS has been used in looking for causative variants and also to hunt for rare variants.

Giving the Keynote presentation on the first day was Prof. Tim Aitman, who told us about:

“Implementing NGS in research and the clinic”

He gave a tour-de-force, ranging from the analysis of NGS data from the genomes of disease model organisms through to the challenges of introducing targeted NGS as a clinical diagnostic tool.

Next up was Clark Mason, presenting on:

“Cell isolation by Flow Cytometry for Next Gen Sequencing and Sequence Detection”

This was a fascinating application talk, describing the power of cell sorting to facilitate sequencing from single-cell genomes.

Dr Jon Strefford told us about the unmet clinical need posed by chronic lymphocytic leukaemia (CLL) and how his lab is performing sequential NGS mutation analysis on single patients during therapy. Furthermore, he described how using NGS can improve prognosis for CLL.

Varsha Khodiyar gave the next talk, telling us about F1000Research, a journal using the Open Access model and how they are campaigning for better access to raw scientific data e.g. from NGS experiments.  Following up on this, as a kind of double-act, Ted Kalbfleisch told us about tools facilitating ways to visualise NGS datasets, that might be useful to peer reviewers and of course, to other scientists.

The lunch-break was a great opportunity to talk to other delegates, browse the exhibitors’ stands and peruse the posters. I got the impression that quite a lot of networking was going on in these breaks – a vital part of any conference.

Nick Downey, from Integrated DNA Technologies, spoke about:

”Enhanced solution based target enrichment using oligonucleotide probes and a novel composition of blocking oligonucleotides”

claiming that their enrichment probes for targeted NGS gave better results on GC-rich sequences than products from rival companies. We also heard about a Cancer gene panel for targeted sequencing of genes involved in acute myeloid leukaemia (AML).

Our next speaker discussed a critical area for clinical genetics:

Simon Patton guided us through the results of an extensive survey of the use of NGS in diagnostic genetics labs in the UK, giving a fascinating picture of  how rapidly the technology is being taken up.  He also emphasised the challenges of assessing the rates of concordance between labs using NGS on the same samples.

Conrad Lichtenstein spoke about technologies developed by Population Genetics:

“Making the most of Sequencing: Accurate targetted sequencing in pooled populations of 1000′s of DNA samples”

One of the approaches that  he described was essentially a very clever way to stick sequence “barcodes” onto long-range PCR products derived from multiple genomes, allowing a very high level of multiplexing.

Our next speaker, from Bio-Prodict,

described how protein structures from non-human species nevertheless can be useful in predicting the effect of human sequence variants, when integrated with other data e.g. from the literature. Furthermore, he claimed that the 3DM platform outperformed well-known tools such as Sift and Polyphen.

The last speaker on day 1 was Kate Thomson, talking about:

“Developing NGS strategies for use in a diagnostic setting”

Dr Thomson returned us to the clinical lab, reminding us of the power of NGS for identifying novel variants, but also the regulatory and ethical challenges it presents.

In my next post, I’ll tell you about the speakers on day 2.

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