Friday, 8 July 2016

Saturday, 9 July 2016

Curtis Huttenhower, PhD
Professor of Biostatistics, Harvard School of Public Health
Presentation Title: The Microbiome Quality Control Project (MBQC).

Abstract: Precision medicine has been made possible by the translation of 'omics' to the clinic, and human microbiome studies must likewise transition to applications in public health. This will require especially robust measurements and assimilation of data from multiple population-scale cohorts. We thus initiated the Microbiome Quality Control (MBQC, http://mbqc.org) project and report a baseline investigation of variability in taxonomic profiling due to physical sample handling, 16S amplicon sequencing, and bioinformatic processing. Blinded sample sets from human stool, chemostats, and mock community mixtures were sequenced by 15 handling laboratories and analyzed by nine bioinformatics protocols. The resulting 16,554 taxonomic profiles were integrated to evaluate the sources and extent of measurement accuracy and variability. Biological variability was typically largest, followed by that from DNA extraction, sample handling environment, and smaller effects from other protocol variables and bioinformatics; almost all factors, however, could produce large effects under at least some circumstances. Quantitative relative measures such as weighted alpha- and beta-diversity were generally robust to bioinformatics methods, but different samples were often differentially affected by individual protocol factors (e.g. DNA extraction effects were largest in fresh stool samples, sample handling environment in negative controls). Analysis of artificial community positive controls revealed systematic differences both in extraction efficiency and in bioinformatic classification, and negative controls identified sources of contamination both in silico and during sample handling. Future evaluations of other microbiome sample types, human body sites, and metagenomic sequencing strategies will be necessary, but these results permit researchers to make informed experimental design choices for gut microbiome studies comparable across labs.

Short Bio: Dr. Curtis Huttenhower is an Associate Professor of Computational Biology and Bioinformatics at the Harvard T. H. Chan School of Public Health and an Associate Member at the Broad Institute. Dr. Hutternhower was the recipient of ISCB 2015 Overton Prize Award. His research focuses on understanding the function of microbial communities, particularly that of the human microbiome in health and disease. His group has worked extensively with the NIH Human Microbiome Project to help develop the first comprehensive map of the healthy Western adult microbiome. As such, his lab develops novel machine learning methodology to leverage structured biological knowledge in high-dimensional genomic data analysis. Dr. Huttenhower received an MS in Computer Science from Carnegie Mellon University and a PhD in Computer Science from Princeton University.

Mick Watson, PhD
Director of ARK-Genomics, The Roslin Institute, Edinburgh
Presentation Title: Can bioinformatics help feed the world?

Abstract: A UN FAO report on the issue of “Food Security” forecasts that global food production will need to increase by over 40% by 2030 and by over 70% by 2050. The objectives of research in farm animals must be to increase yield, disease resistance, food production, food safety and quality and to decrease infections, water use, energy use, the environmental impact and the chance of zoonoses. Genomics technologies are becoming increasingly critical in the pursuit of these goals, and second and third generation sequencing technologies have fuelled a revolution in biological research. I will present results from a range of collaborative research projects that demonstrate the power of sequencing technologies and bioinformatics, including the use of metagenomics to investigate the rumen gut microbiome, with impacts in novel enzyme discovery, methane emissions and food production.

Short Bio: Dr. Mick Watson is an established bioinformatician, with 15 years’ experience in industry and academia. He was involved in the implementation and management of pipelines for functional genomics at GlaxoWellcome, SNP discovery at Incyte Genomics and Target Discovery at Paradigm Therapeutics, before joining the Institute for Animal Health as Head of Bioinformatics in 2002. He has been Director of ARK-Genomics since July 2010, and has won several grants to create a bioinformatics research group allied to the ARK-Genomics facility. His group's research focuses on the use of computational and mathematical techniques to understand genome function with an emphasis on systems of relevance to animal health and food security. Publications include both primary bioinformatics research papers and collaborative research in a variety of technical and scientific journals. The outputs from his research have included novel algorithm development, as well as the application of bioinformatics techniques to microbial and meta-genomics.