Day 2 kicked off on time with a full house for the first presentation of the day by Neil Hall on aspects of microbiome sequencing as well as the diverse sequencing capabilities of the Centre for Genomic Research in Liverpool. Neil mentioned that they tackle specialist problems using their expertise and the he spent some time introducing the technology behind the Pacbio sequencing platform. This was an interesting talk especially as none of the clinical genetics groups present had used this platform in house. Neil spoke about the improvements that had been made over the years to make it a more robust sequencing platform. Neil’s presentation was followed by that of Sarah Ennis who spoke about the capabilities of their sequencing facility as well as their multidisciplinary approach with their use of one of the most powerful supercomputers in Europe. Sarah also spoke about the quality aspects in relation to sequencing especially how their quality workflows were able to identify contamination; this was followed by an overview of their work on clinical patient samples from diverse diseases areas including primary immunodeficiency and complex autoimmune disease.
Matt Zilbauer from Addenbrookes Hospital presented an excellent talk on Inflammatory Bowel Diseases (IBD) such as Crohn’s disease and Ulcerative Colitis and their link to factors that arise from an individual’s modern life style. Matt cited an increasing incidence of IBD in developing nations whose life styles were becoming more modernized and used to this to say that the environment was a major driver of disease pathogenesis. There were then specific examples of epigenetics as the interface between the environment and the genome where Matt spoke about studies that his group had done using DNA Methylation intestinal health and immune mediated disease. Matt’s talk was followed up by another talk on Epigenetics by Santiato Uribe-Lewis on cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia and looking at colon cancer tissues. The last talk of the morning session by Mick Watson was introduced by Bas Vrolling. Mick gave a very good overview about the capabilities and latest work by the Edinburgh Genomics group on exomes, transcriptomes, genomes, epigenomes and metagenomes.
Melanie presented their NGS facility’s capabilities in a variety of applications including transcriptome sequencing, epigenetics, amplicon sequencing and re-sequencing for a plethora of species ranging from microbes, plants, animals and humans. Geoff Barton then spoke about RNA Seq and how different data analysis methods had produced differing conclusions on gene expression levels; Geoff attributed these to a potential lack of a high number of replicates due to the still high cost of sequencing and then discussed their own work where they had carried out a high replicate RNA Seq project. Martin Taylor then spoke about his work to quantify and understand how WGS compares with the targeted capture and sequencing of the exome (exome-seq), for the specific purpose of identifying single nucleotide polymorphisms (SNPs) in exome targeted regions. Chris Cole then presented results from four human samples run against Illumina’s Nextera, Agilent’s SureSelect v5 and Nimblegen’s SeqCap v3 sample preparation kits and sequenced across four lanes of a HiSeq2000, highlighting differences between the kits.
This concluded the NGS 2014 Dundee conference and it was agreed to reconvene in 2015.