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Ahoj! From Prague and the EMEA ISS 2014

by
Lukas Smink, Ph.D.
| May 15, 2014
Illumina's European Scientific Summit was held in the historic city of Prague

Day one of the EMEA Illumina Scientific Summit in Prague focused heavily on life sciences research as well as new and emerging opportunities. Dr. David Bentley (Illumina VP and Chief Scientist) started the meeting together with Dr. Lucy Raymond (Reader in Neurogenetics and a Consultant in Medical Genetics).  David set the stage for Lucy on the progress of sequencing in a healthcare setting and what individual genome sequencing could offer, all the way from pre-implantation and newborn screening to cancer sequencing at key time points of disease progression, and targeted follow up to detect residual disease. Lucy highlighted that in the UK, 0.5% of the population has a rare genetic disease. What shouldn’t surprise me but never fails to, is that 50% of all childhood hospital admissions are associated with rare Mendelian disease. Lucy posed the question of why study these very rare diseases when they affect so few individuals. Other than understanding the underlying biological mechanism and potential therapeutic indications, the key argument is that for most patients and their families, getting a diagnosis is in itself a therapeutic.

Currently in the UK, a clinical service for ~1,000 genes is available through one of the 24 clinical genetic centres. These centres are well-linked and have standardised investigation procedures, however these assays are by no means comprehensive. There are a number of projects under way, such as the UK 10K, which aims to study all of the genetic information in 10,000 people. Of the 10,000 participants, 4,000 will have their full genome sequenced and the remaining 6,000 will undergo exome sequencing. The other UK-wide study is DDD (Deciphering Developmental Disorders) project which aims to perform exome sequencing of 4,000 parent –child trios. Last but most certainly not least is the Genomics England project to sequence 100,000 Genomes , which aims to prime to pump for the increasing the utility of genomics in the UK health service (NHS).

Sheila Fisher, the Director of Operations and Development at the Broad Institute talked about her team's experiences and early data from the NextSeq 500 and the HiSeq X Ten. The Broad is currently producing 2 Tb per day but with the HiSeq X they expect that to scale to 6 Tb. If you think those are large numbers, the Broad sequenced 44,130 exomes, 2,247 genomes, and 8,189 RNA-Seq samples as well as other samples using applications such as 16S sequencing last year. In the data comparison, Sheila highlighted very similar data coming from both the NextSeq and HiSeq X compared to the HiSeq 2500, along with very similar sensitivity and precision to detect variants. On the HiSeq X, they have production data from 100 genomes thus far, with 500 genomes in line for sequencing and 2,000 more moving through sample prep.

Miodrag Grbic discussed whole-genome sequencing of the spider mite, a common agricultural pest. The study of the spider mite is a model for Chelicerata, a subdivision of arthropods that includes spiders, scorpions, mites, and ticks. Reasons to study the spider mite extend past understanding the pest, including being easy to propagate in the lab, and having a relatively short embryogenesis. While the genome is relatively small, it features a large expansion of detoxification gene families, which may offer an explanation of why the spider mite develops such quick resistance to pesticides. A side discovery of the project was uncovering amazing properties of spider mite silk, which could potentially lead to a novel bio-nano material.

After lunch, James Hadfield spoke on monitoring cancer genome evolution through the use of circulating tumour DNA (ctDNA). The use of liquid biopsies could allow unbiased disease detection and monitoring, and various research groups have shown that there is a correlation between the levels of ctDNA with clinical outcome of the disease. Tomas Marques highlighted some potential pitfalls in detecting copy number variants (CNVs). The fine scale structure of the genome will reveal important biological aspects, and long sequencing reads will be instrumental in driving future discoveries.

The final customer talk of the day was by Brendan Keating who discussed the genomic underpinnings of transplant rejection and its associated complications. Brendan highlighted that for most patients a transplant procedure, even if successful, is no guarantee. Generally the organ lasts only a number of years before another transplant is required. The list of patients is continually growing. A large international consortium is bringing together many different groups to study genetics of transplantation, so we eagerly anticipate new research in this area.

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