Generating genomic level data just got easier, by the introduction of benchtop sequencers like MiSeq and IonTorrent PGM. The amazing thing is just a decade ago it took us nearly 3 billion dollars to sequence the complete human genome. Now these machines are making the $1000 genome a reality.
Illumina’s MiSeq, a desktop DNA sequencing machine priced at $125, 000, promises to speed up Next Generation Sequencing (NGS). The technology is based on optical detection of the four fluorophores that are incorporated into DNA during synthesis of the DNA polymer. The workflow integrates clonal amplification, paired end module, sequencing, base-calling and data analysis in a single instrument. MiSeq’s personal sequencing system enables researchers to go from sample to analyzed data in just 8 hrs.
Life Technologies introduced Ion Torrent PGM (Personal Genome Machine) and more recently the Ion Proton Sequencer, another ‘benchtop’ sequencer priced as low as $50,000, uses a pioneering new approach to DNA sequencing using the highly scalable ion semiconductor technology that revolutionized the computer industry.
The figure shows how hydrogen ions that are released during the polymerization of DNA indicate if one or more nucleotides got incorporated into the growing DNA chain. The released ions change the pH of the solution that is detected electrically by ISFET (Ion-sensitive field effect transistors) sensors. Mulitple incorportations lead to corresponding number of released hydrogens and the intensity of the signal. The high density array of wells on the Ion semiconductor chips provide millions of individual reactors while integrated fluidics allows reagents to flow over the sensor area.
The interesting thing is that all the biology happens on the chip and apparently the newest Proton 2 chip is designed to hold half a billion wells. This unique combination of fluidics, micromachining and semiconductor technology enabled the direct translation of genetic information (DNA) to digital information (DNA sequence).
The major advantage of this technology is rapid sequencing speed and low upfront operating costs. If the semiconductor chips are improved (as per Moore’s law), the number of reads per chip should increase. As of Aug 2011, the read length is 250 bases in 2 hrs and the accuracy is 99.6%. But unlike MiSeq, in Ion Torrent, after library preparation, one must clonally amplify with emulsion PCR prior to sequencing.
As these tools become mainstream in more and more labs, the hope is that it will prove to be beneficial for personalized medical applications rather than generate more mindless data. The questions being asked range from ‘what will be the future role of core facilities that offer sequencing services?’ to ‘how to make meaningful sense of the data?’ It appears that core facilities will need to gear up to analysis rather than the current focus on data generation. Exploring these massive datasets to glean biologically relevant insights has been the bottleneck in this sequencing race. Strand Life Sciences proprietary Avadis NGS software (http://www.avadis-ngs.com/) works to bridge this gap and can be used to analyze both data coming from MiSeq and IonTorrent. It helps identify significant SNPs with high confidence using a intuitive filtering framework and perform structural variant analysis on the DNA sequence data. The aligner that they call as the COBWeb feature aligns long variable length reads allowing for arbitrary gaps and mismatches. Multiple alignments can be visualized in a Genome Browser. The sequence data can also be connected to GO and Pathway analysis. If you are looking for open source software, one place to start would be the IGV (Integrative Genomics Viewer) tool offered by Broad Institute, a visualization tool for interactive exploration of large genomic datasets.
Bioinfoworld 
Leave a comment