Kashi Clinical Laboratories offers a wide range of cutting edge platforms and services to help meet your requirements.  Our scientific professionals routinely undergo extensive training on the latest technologies and maintain stringent requirements as a CLIA-certified laboratory and Certified Services Provider of Ion Torrent.

Next Generation Sequencing

Kashi Clinical Laboratories offers Next Generation Sequencing (NGS), using both Ion Torrent and Illumina platforms, including the Ion Torrent S5, Proton, PGM and MiSeq 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.

Ion 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 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 (SNV’s) and small insertions and deletions (indels) in protein coding genes
  • 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)
  • Ion S5 (similar capacity to the Proton, but streamlined for more automated workflows with cartridge-based reagents)
  • Illumina MiSeq (cartridge-based reagents with samples loaded onto a flow-cell, capable of paired-end reads and up to 15 Gb per run)

Capillary Electrophoresis

Kashi Clinical Laboratories is an independent CLIA-approved lab for capillary electrophoresis. Using the U.S. Food and Drug Administration-3500xl Dx Sanger sequencing platform to detect and identify fluorescence-labeled DNA, Kashi offers precise capillary electrophoresis. Standard four-color fluorescent labeling, where each color represents one of the four DNA bases, is widely recognized as the preferred detection method for automated capillary electrophoresis platforms. Using capillary electrophoresis, Kashi’s scientists can provide you with faster results and high-resolution separation.

Capillary electrophoresis is an analytical technique that separates ions based on their electrophoretic mobility, with the use of an applied voltage. The electrophoretic mobility is dependent upon the charge and size of the molecule. The rate at which the particle moves is directly proportional to the applied electric field: The greater the field strength, the faster the mobility.

Neutral species are not affected; only ions move with the electric field. If two ions are the same size, the one with greater charge will move the fastest. For ions of the same charge, the smaller particle has less friction and overall faster migration rate.

Kashi offers:

  • In-vitro diagnostics for HLA
  • Fragment analysis (microsatellite analysis) (non FDA use)
  • de novo sequencing and re-sequencing (non FDA)

3500xl Dx specifications:

  • IVD (21CFR) compliant system can be used for data intended for FDA submissions
  • IVD (21CFR) validated system software that provides real-time data collection, security, audit and electronic signature features
  • RFID (radio frequency identification) for tracking key consumables and record administrative information
  • IVD labeled reagents
  • 24-capillary array with thermal system design for demanding DNA fragment analysis

Quantitative Real-Time PCR

Using the latest in qPCR instrumentation, Kashi Clinical Laboratories has the flexibility to perform SNP genotyping, NGS library quantitation, CNV determination, gene expression and miRNA profiling. The QuantStudio 6 enables detection of as low as 1.5-fold changes in single-plex reactions and has a 10 log dynamic range allowing for great sensitivity. This instrument also allows for an interchange between 96-well and 384-well formats to accommodate low or high sample throughput provides accurate measurements of nucleic acid concentrations using quantitative polymerase chain reaction (qPCR) in real time. The quantitative measurement is collected during the log phase of PCR amplification, when the quantity of PCR product is directly proportional to the amount of template nucleic acid. With qPCR’s high dynamic range, we can provide detection down to a two-fold change in concentration or quantitation of RNA from a single cell.

A quantitative real-time polymerase chain reaction is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR), which is used to amplify and simultaneously quantify a targeted DNA/RNA molecule. For one or more specific sequences in a DNA/RNA sample, quantitative PCR enables both detection and quantification. The quantity can be either a concrete number of copies (absolute quantitation) or a relative change in DNA/RNA concentration when normalized to DNA input or additional normalizing genes (relative quantitation).

The procedure follows the general principle of polymerase chain reaction. Its key feature is that the amplified DNA is detected as the reaction progresses in “real time.” This is a more precise approach compared to standard PCR, where the product of the reaction is detected at its end.

RT PCR Applications:

  • Gene expression Analysis
    • Quantitation of gene products (or quantitation of gene expression)
    • Microarray verification
    • Pathway analysis- gene expression/suppression triggers
    • siRNA/RNAi
    • Low-fold copy number discriminations
  • Micro RNA and Non-coding analysis (genomic regulation)
  • SNP Genotyping
  • Pathogen detection


Using Luminex’s flexible xMAP platforming technology, Kashi Clinical Laboratories offers a variety of assay techniques. With its open architecture, Luminex provides for quick and accurate analysis.

Up to 500 polysterene microspheres, each containing red and infrared fluorophore dyes, can be present in a single well. The different combinations of red and infrared dyes within each microsphere offer a unique spectral fingerprint that is recognized and classified by the instrument, allowing for accurate analyte discrimination and analysis. The 3-D surface chemistry of each microsphere, which could consist of antibodies, receptors, peptides, or oligonucleotides, allows for expedited chemical coupling of capture reagents through solution-phase kinetics.

The benefits of Luminex include:

  • High throughput – maximum of 500 analytes can be multiplexed at once (per sample) in each reaction well of a 96-well PCR plate. (500 tests per sample)
  • Less sample volume needed per reaction due to multiplexing abilities
  • Comparable results to ELISA and Microarrays in much less time and with less labor
  • Extremely versatile, with numerous applications and assay capabilities
  • Can be customized to meet the needs of the consumer through different microsphere-to-probe attachments

The applications of Luminex include:

  • DNA assays
  • Immunoassays
  • Receptor-ligand assays
  • Enzyme assays
  • HLA testing and HLA antibody testing
  • Protein expression profiling
  • Gene expression studies
  • Drug discovery: Pharmacogenetics and proteomics