Poster: Exome Sequencing with Ion Torrent and Pippin Prep

In a poster from Ion Torrent (Life Technologies) for 2012’s ASHG, scientists looked at exome sequencing by studying a familial trio on both the PGM™ and the Proton™ instruments. Size selection for both sequencers was performed on the Pippin Prep from Sage Science.

Using an enrichment process targeting protein-coding exons from various genetic databases (including GenCode, RefSeq, Ensembl, and others), the scientists report “an on-target read mapping rate of 80%.” The sequencing, which took about four hours on either instrument, generated more than 5 Gb of aligned sequence, with average depth greater than 50x.

The Life Technologies authors note that they used Pippin size selection for both instruments, selecting an average length of 200 bp for the Proton and 300 bp for the PGM. (Check out figure 3 of the poster to see the nice clean peak they generated with Pippin.) This step was followed by exome enrichment and amplification prior to sequencing. The results indicate that sequencing exomes on the Proton is better than five times more efficient than on the PGM, and the authors say that stat is expected to improve even more.

Overall, the authors say, this study demonstrates that “the combination of focused exome enrichment and Ion Torrent Systems-based sequencing and analysis provides an efficient, accurate, and rapid means to detect genetic variation in the well-annotated portion of the genome for state-of-the-art genetic disease research.”

Check out the poster here.

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