“Now” generation sequencing has drastically changed the traditional costs and infrastructure within the sequencing community. There are several technologies, platforms and algorithms that show promise, but it is not always intuitive where to start. This uncertainty is compounded by the fact that commonly used analysis tools are difficult to build, maintain, and run effectively. Sample acquisition and preparation is quickly becoming a bottleneck as projects move from small sample sizes to hundreds or even thousands of samples. We will present case studies highlighting information, methods, challenges and opportunities in leveraging large scale high throughput sequencing and bioinformatics. Specifically we will highlight a recent genome-wide study of methylation patterns in 1575 individuals with Schizophrenia. We will also discuss several cancer transcriptome and exome sequencing projects as well as a human pathogen transcriptome characterization project consisting of multiple organisms and almost a billion reads.
The Ion Torrent PGM machine is a very promising, rapid throughput, ultra scalable sequencer that could play an integral part in future human health studies. Applications such as microbial whole genome sequencing, metagenomic characterization of environmental and microbiome sample, and targeted resequencing projects stand to benefit from this technology over time. To date we have completed more than 25 runs on a single PGM and will comment on the setup as well as sequence data and analysis.