Platforms and Capabilities

Next Generation Sequencing

Kashi Clinical Laboratories offers Next Generation Sequencing (NGS), using the fastest in Ion Proton and Ion Personal Genome Machine systems. With the ability to rapidly generate large volumes of sequencing data, NGS enables health professionals to move quickly from one idea to full data sets. NGS is highly scalable and, because it can be tailored to any given experiment, provides a high degree of flexibility when it comes to viewing high- and low-level resolutions.

NextGenSequencingIon Torrent Next Generation Sequencing (NGS) utilizes a semiconductor-based, sequencing-by-synthesis technology and emulsion PCR (emPCR) similar to other platforms. It measures the H+ ions released during base incorporation.

Bases of small fragments of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a DNA template strand. NGS extends this process across millions of reactions in a massively parallel fashion, rather than being limited to a single or a few DNA fragments. This advance enables rapid sequencing, or large stretches of DNA base pairs spanning entire genomes, with the latest instruments capable of producing many gigabases of data in a single sequencing run.

For example, consider a single genomic DNA (gDNA) sample. The gDNA is first fragmented into a library of small segments that can be uniformly and accurately sequenced during millions of parallel reactions. The newly identified strings of bases, called reads, are then reassembled using a known reference genome as a scaffold (resequencing) or in the absence of a reference genome (de novo sequencing).

Applications for NGS include:

  • Targeted sequencing for DNA and RNA
  • Exome sequencing, enabling identification of single nucleotide variants (SNVs) and small insertions and deletions (indels)
  • Transcriptome sequencing (RNA sequencing can quantitate changes in gene expression, as well as detect fusion transcripts from chromosomal rearrangements)
  • Genome sequencing, including de novo sequencing, bacterial typing, and viral typing
  • Aneuploidy detection (Large chromosomal duplications or deletions and copy number variations (CNVs))
  • Epigenetic Applications (Chromatin Immunoprecipitation sequencing).
  • Microbial Population Analysis, including metagenomics and viral, bacterial, and yeast genome sequencing

Instrument specifications include:

  • Ion Personal Genome Machine (small genome sequencing or targeted DNA and RNA sequencing)
  • Ion Proton (comprehensive exome sequencing, using larger chips with higher densities for exome and whole genome sequencing)