Next-Gen Sequencing

The Genome Core hosts Next Generation Sequencing on the Ion Torrent Personal Genome Machine (Ion PGM) platform. The instrument is versatile in the clinical research environment with various applications that it can perform (listed below). The bread-and-butter of the instrument is in its capacity to perform fast and precise workflows using the Ampliseq technology. With the hands-on time included, as well as automation, sequencing time and data acquisition, the entire workflow can be done in 3-5 days. Particularly helpful in a clinical environment are the pre-existing secondary data analysis options available through Ion Reporter, if you are starting from human or mouse samples.  For the most basica analyses, such as variant calling or a tumor/normal comparison, you won't need additional bioinformatic support.  You can do it on your own.  Feel free to email the Core about any questions regarding sequencing projects. 

Targeted resequencing of oncogenes and somatic mutations:

The Ion Torrent PGM is capable of streamlining the process of resequencing by incorporating pre-made Ampliseq panels for thousands of prominent biomarkers. For example, the Ion Ampliseq Cancer Hotspot Panel v2 sequences ~2800 mutations within 50 hotspot oncogenes. Refer to this page for the list of genes and mutations that are included using the Ion Ampliseq Cancer Hotspot Panel v2. For even greater gene coverage, the Core also hosts the Ion Ampliseq Comprehesive Cancer Panel, which sequences over 400 genes. If needed, custom-made panels can be prepared to meet external needs. 

Additional applications

The Core can also assist in projects utilizing custom, targeted applications of the Ion Torrent platform, including both DNAseq and RNAseq.  Unique applications exist, such as

  • cell-free DNA panels
  • immune response expression profiling

Chip capacities: 

  • 314 Chip: 40Mb, 200bp average length, 500k reads per chip
  • 316 Chip: 400Mb, 200bp average length, 2-3 million reads per chip
  • 318 Chip: 1Gb, 400bp average length, 600 million to 1 billion reads per chip.

We currently offer hands-on training in the theory and practice of second generation sequencing. At the end of our laboratory training, offered on demand, you will be able to independently perform your own sequencing.