Tools, technology, and analyses: All present and accounted for at Genome Informatics 2016

By Michael Campbell

This years meeting was held in the UK at the Welcome Genome Campus in Hinxton.  Several speakers addressed the idea that no variant is an island in the Personal and Medical Genomics session. Variant centric approaches to interpreting genetic variation are unable to predict the effect of multiple variants on a given haplotype. Sever plugins for Ensembl's Variant Effect Predictor (VEP) were presented as talks and a new tool called ICE (Interpreting Changes to Exons) was presented as a poster (by me ). 

ICE development is driven by a collaboration between members of the Gramene development team at Cold Spring Harbor, Tim Reddy's group at Duke, and  Mark Yandell’s group at the University of Utah. A special thanks to Bill Majoros in the Reddy lab for driving the code development. Gramene’s role in this collaboration is to ensure ICE is developed to be aware of plant biology and evaluate the utility of this approach to characterizing population level variation and the impact of these variants on gene function in crop species.

The Variant Discovery And Genome Assembly session started out on a high note with the report of nanopore sequencing with 90% base calling accuracy off of the machine and 99.95% consensus accuracy given 80X coverage. We may have gotten a glimpse of the low cost, high-quality long-read unicorn.

The limitations of a linear reference genome were showcased as variant graphs and presented as an alternate representation for reference genomes. This theme continued as RUFUS, a reference free method for variant detection, and Pizzly extension of Kallisto, a reference free method for detection and quantification of fusion genes, hit the stage.

The sustainability of the manual literature curation efforts was brought in to question and then carefully dissected. This dissection revealed that a sustainable future for the manual literature curation of UniProt is feasible and sustainable, but perhaps slightly out of reach at current funding levels.

Single-cell transcriptomics, metagenomics, cancer genomics, and a variety of evolution informed analyses rounded out the meeting. Research questions ran the gamut of horizontal gene transfer, early human history, gene regulation, and more.

The challenges facing the leading edge of genomics were highlighted throughout the meeting. New tools and technology are being brought to bear on these challenges giving us all greater insights into the complexity and wonder of biological systems.