The DNA Analysis Facility at Sanford-Burnham in La Jolla provides next-generation sequencing services, from experimental design to data analysis. The facility has two next-generation sequencers, the Life Technologies Ion Torrent PGM and Ion Proton sequencers. Both platforms offer rapid turnaround, with sequencing run times ranging from 2-7 hours. The Ion Torrent can provide up to 1 Gb of sequencing data, with reads up to 400 bases in length. The Ion Torrent is ideal for sequencing of small genomes and targeted sequencing of predefined gene sets, such as mutations in genes associated with cancer. The Ion Proton currently produces up to 10 Gb of sequence data with read lengths up to 200 bases and will support several applications including, whole transcriptome, and whole exome sequencing. The P II chip for the Ion Proton, scheduled for release by September 2013, has an advertised output of 30 Gb, sufficient for whole genome sequencing. As a core facility, the sequencing facility provides state-of-the-art equipment and expertise, which would be impractical for individual labs to maintain. The core also provides sequencing services to investigators outside of Sanford-Burnham.
Included in the cost of sequencing is basic bioinformatic analysis (SNP/InDel calling, transcript abundance). The core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing. Advanced bioinformatic and systems biology analysis is available through the Bioinformatics & Data Management core in La Jolla.