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ESHG 2014 Day One Summary

by
Scott Brouilette, Ph.D.
| Jun 01, 2014

Having enjoyed the ESHG Satellite Symposium on Friday, we headed to the opening sessions of the ESHG which, somewhat bizarrely, happen before the official opening of the conference!

No matter – we simply had to attend a session entitled “What’s new in NGS”.  Alex Hoischen (Nijmegen) got us started by considering novel approaches to study genetic disease. His opening comment was certainly one that reminds us immediately of the fragility of our health: “we have 6 billion nucleotides, but just a single variant has the potential to cause disease”. Sobering indeed. Alex took us though his experiences of identifying disease-related genes, praising exome sequencing as “revolutionary” in this context, while at the same time stating that there is room for improvement as all current methodologies miss a certain percentage of coding regions. He also highlighted a genotype/targeted sequencing approach before detailing the use of molecular inversion probes (MIPs) for target capture of 1-100 genes in 96 samples over 2 days. Alex then moved onto “New Technology & Methods”, but didn’t show anything an NGS-aware audience didn’t already know . The key slides related to long reads and the applications they enable, and Alex did remind the audience of the long-reads technology from Illumina, formerly known as Moleculo.

The Science for Life Laboratory (SciLifeLab) introduced what many feel is the most interesting development in NGS – single-cell sequencing. This was voted Method of the Year 2013 by Nature Methods, and has applications ranging from cancer, immune cell biology, rare cell identification within the microbiota and more. This technology is becoming more accessible due to a combination of microfluidics and the decreasing cost of sequencing. After reviewing the methods, 1,2  the question was asked: does a single cell actually contain too much information? To combat this concern, the use of single-cell panels was suggested. But the flourish in the talk was the overview of the “spatial transcriptomics” method the guys at SciLifeLab have developed: using barcoded solid phase cDNA sythensis followed by sequencing ~135,000 barcoded features (i.e. transcripts) were interrogated across thousands of cells in a single experiment. Using a custom cloud-based tool, a user can select a gene from a drop-down menu and see the spatial distribution, for example, across an entire histological section! This type of methodology certainly has great potential in a clinical setting, potentially making good use of existing histological blocks/section currently residing in freezers around the world.

After a quick break, we were treated to the plenary session, including interesting talks from Marco Tartaglia on ras dysfunction, and Allessandro Biffi on HSCs for treatment of inherited disease. The highlight was Elena Cattaneo telling us about the Huntington’s Disease (HD) gene. Elena was voted the 2013 Stem Cell Person of the Year Award, and was appointed to the Senate of Italy as a Senator for life, the youngest in Italian history, by President Giorgio Napolitano on 30 August 2013. Impressive credentials, and a suitably impressive presentation followed. Like many people I spoke to after the session, I had assumed that HD was essentially a binary outcome – you have it or you don’t. But Elena eloquently educated us – the variable number of CAG repeats in the huntingtin (htt) gene is key. Over 36 of these repeats is causative, and an intermediate number (17ish – 35) can cause problems, but a lower repeat number (but very rarely under 9 in humans) and there is no disease. But the key questions were: why do we all carry the HD gene? And why this variable repeat number? It turns out that htt is important for brain function, has anti-apoptotic roles, is involved in axonal transport and in BDNF vesicle transport. It also plays key developmental roles including gastrulation and nutrient trafficking. Interestingly, unicellular organisms do not have htt, with the CAG repeats (n=2) first appearing in the sea urchin. Repeat number varies across species (4-8 in zebrafish, 9-35 typically in humans), and Elena has attempted to link these species-specific ranges to behavioral traits, such as snowball-play in Japanese macaques, but failed to show any correlation on that one! Perhaps even more interesting is the correlation of higher CAG repeat number with increased amounts of grey matter, really highlighting the selective pressures that may have shaped CAG repeats during evolution.

We then broke into separate streams for the remainder of the day; these will be summarized in a separate post. Summaries from the Personalised Medicine and Pharmacogenomics and Cardiovascular rapid-fire lectures below are from myself and several colleagues.

Personalised Medicine and Pharmacogenomics

Melissa Sorosina studies variation in response in interferon-treated multiple sclerosis patients and described a GWAS using the Illumina 660 quad chip with one major hit, rs9828519, located in SLC9A9. This sodium-hydrogen exchanger is up-regulated by IFN-beta, and in silico analysis revealed a number of putative interferon-sensitive response elements (ISREs) in the promotor region of SLC9A9.

Marieke Coenen talked about thiopurine dosing and the potential for serious side effects in patients with IBD. By genotyping for thiopurine methyltransferase (TPMT) they were able to personalize the type and dose of thiopurine. In a study of 769 patients, this lead to a significant reduction in the incidence of leukopenia, the primary problem with inefficient thiopurine treatment.

The session ended with MS Meyn and the issues of introducing personalized medicine in a pediatric setting. By piloting the use of WGS as a diagnostic test in the SickKids Genomics Clinic, they found that the primary obstacle was not technical in nature. Obtaining informed consent from BOTH parents proved the key issue, with the speaker emphasizing the need for open dialogue between the parents and the physician throughout the entire process. Despite this difficulty, 174 out of 321 families approached had enrolled in the study, and at this time 50 subjects had undergone WGS. From just the first 12 genomes 5 novel diagnoses had already been made.

Cardiovascular Disorders

The session started with Melanie Eyries detailing her team’s work on pulmonary veno-occlusive disease (PVOD). PVOD can be either a familial or sporadic disease; in France, Melanie has identified 5 families and performed exome-sequencing of 2 unaffected and 3 affected siblings per family using Illumina TruSeq Exome Enrichment on HiSeq. Using an informatics pipeline including CASAVA, Samtools, and  Annovar they have identified mutations in GCN2, the first time a genetic component has been demonstrated in the context of PVOD. They went on to identify 22 different variants in GCN2 and showed that such mutations were responsible in 100% of familial cases, and 25% sporadic cases of PVOD.

Following on was S. Al Turki looking at human congenital heart defects (CHDs) in conjunction with SickKids (Toronto), Sanger (UK) and the Medical Research Council (MRC). CHDs are not uncommon, at 8 in 1,000 live births, and contributes to 1/3 of neonatal deaths. An exome-sequencing approach in 13 trios and 112 unrelated subjects identified NRF2F, a pleiotropic transcription factor as a primary candidate, likely impacting fetal heart and aorta development.

Sara Bardi and colleagues ended the session looking for variants with potential roles in hypertrophic cardiomyopathy (HCM). Mutations in sarcomeric genes have been identified in 64% of HCM cases, and a custom targeted re-sequencing panel of 111 genes designed with DesignStudio and run on the HiScan HQ revealed additional variants in desmosomal genes.

References:

1. Eberwine, J., Sul, J.-Y., Bartfai, T. & Kim, J. The promise of single-cell sequencing. Nat Methods 11, 25–27 (2014).

2. Wu, A. R. et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 11, 41–46 (2014).

 

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