Custom Next Generation Sequencing Assays to Support Drug Development.
Next Generation Sequencing Using the Life Technologies Ion Torrent PGM™ or Roche 454 GS Jr.™ Systems
AltheaDx provides next generation sequencing services using both the Life Technologies Ion Torrent PGM™ system and the Roche 454 GS Jr.™ system. AltheaDx provides a total workflow solution starting from nucleic acid isolation, target enrichment, library construction and sequencing for applications such as RNA-seq, target resequencing and amplicon sequencing.
AltheaDx utilizes established target enrichment strategies to optimize sequencing depth of coverage across the specific regions of interest, allowing for accurate mutational analysis by massively parallel sequencing. Hybridization based selection methods (i.e. Halo Genomics Selector, Agilent Sure Select, Roche SeqCap or Ion Torrent Target Capture) or amplicon based selection methods are designed specific to the sample type and disease indication. Libraries of specific regions of interest are sequenced to an optimal depth and data analyzed for genetic variants. Transcriptome sequencing of ribosomal depleted, small RNA (miRNA), polyA selected or transcript specific RNA can provide sensitive expression profiling, alternative promoter and splice variant data.
The Ion PGM™ pairs semiconductor technology with a sequencing chemistry that exploits the release of a hydrogen ion, and therefore a pH change, when a nucleotide is incorporated into a growing strand of DNA by a polymerase in a high-density array of micro-machined wells to perform this biochemical process in a massively parallel way. Each well contains an emPCR clonally amplified DNA template. Beneath the wells is an ion-sensitive layer and with a proprietary Ion sensor. The Ion PGM™ system delivers a throughput of ~100 million* high-quality, filtered bases per run; average read length: ~100 bases with 99% accuracy. Turnaround times for deep sequencing can be as short as 1 day.
The Roche GS Junior Sequencing System utilizes a parallelized version of pyrosequencing (454 pyrosequencing). Similar in methodology, the sequencing apparatus contains many picolitre-volume wells each containing a single bead with a clonally amplified DNA template on a bead. The Roche GS Junior delivers a throughput of ~35 million high-quality, filtered bases per run; average read length: ~400 bases with 99% accuracy at 400 bases; 100,000 (shotgun); 70,000 (amplicon) reads per run. Turnaround times for deep sequencing can be as short as 10 days.
*100 Mb with existing Ion PGM™ system “316″ chip expanding to 1Gb in 2012 with “318″ chip.