A GENOMIC assembly technology using a flow-based detector promises a cheaper approach to DNA sequencing, as the instruments and reagents required are much less expensive, says SoftGenetics. Its Ion Torrent PGM sequencer is based around a silicon chip made up of several million individual pH sensors, which respond to the hydrogen ions released during incorporation of unmodified nucleotides in DNA replication.
Although this so-called ‘post-light’ approach offers economic benefits, it does present a challenge in error correction. Most errors manifesting through the system are insertion/deletion errors (indels), rather than substitution errors. This is particularly true in homopolymer regions, says the company.
Indels are more problematic for assembly, because of the higher complexity of gapped comparison, says Dr Jonathan Liu, VP of development at SoftGenetics. “NextGene software includes a flow-based assembler, Floton, which can treat homopolymer errors as substitution errors during the assembly process. The method condenses the sequence into flow calls of individual bases, and bases in each flow. By converting the sequence data to flow format, essentially the indels are converted into substitution errors, allowing for more accurate and faster assembly”.
Megan Manion, NextGene technical product manager, added: “In practical application, Floton users are experiencing substantial increases in assembly accuracy compared to base-space assembly”. SoftGenetics offers a 30-day trial and free web-based training on its genetic analysis software.