Systems and Software

What is mass spectrometry and how is it used in your systems?

Mass spectrometry is an analytical chemistry technique that identifies the amount and type of molecules present in a sample by measuring the mass-to-charge ratio and abundance of gas-phase ions.

At Agena Bioscience, we utilize a specific type of mass spectrometry, matrix-assisted laser desorption/ionization time-of-flight, or MALDI-TOF, mass spectrometry. Although MALDI-TOF mass spectrometry is widely used for proteomics applications such as peptide mass fingerprinting, Agena Bioscience is one of the few companies that has adopted MALDI-TOF mass spectrometry for genomic applications to analyze nucleic acids.

The application of this technology and the direct detection of nucleic acids enables the use of the MassARRAY® System for high multiplex capability and sensitivity.

What is included with the MassARRAY System?

The MassARRAY System includes the mass spectrometer, computer/server, and analysis software. Customers who utilize the 96- and 384-well formats of the system will also most often receive a Nanodispenser RS 1000.

How many samples can be processed on the MassARRAY System?

The MassARRAY System throughput depends on the assay design and the format of SpectroCHIP® Array (chip) being utilized. The MassARRAY System processes 2 chips per run.

The chip comes in one of three formats, 24-, 96-, or 384-well format. If the assay design calls for a single well, the number of samples processed in a single run ranges from 768 samples with the 384-well format chips to 48 samples with the 24-well format.

What is included for the maintenance of the MassARRAY System?

Each new system is covered by a one-year warranty and one year of maintenance. Extended plans are available. Please contact Customer Support for more information.

What is the Nanodispenser RS 1000?

The Nanodispenser RS 1000 is an automated platform that transfers analyte from a microtiter plate to the SpectroCHIP Array.

Does the 24-well format of the MassARRAY System include the Nanodispenser RS 1000?

No, the 24-format requires manual dispensation of 0.75 microliter volumes. Currently the Nanodispenser RS 1000 is available with the 96- and 384-well formats which require nanoliter volumes.

What is the SpectroCHIP Array?

The SpectroCHIP Array (chip) is our proprietary chip technology onto which analyte is transferred once the PCR and extension/cleavage steps are complete. The chip comes in one of three formats, 24-, 96-, or 384-well formats.

What is a raster, and how is it used?

A raster is a single point within a pad on the SpectroCHIP Array at which the laser in the MassARRAY System is shot. To acquire spectra suitable for analysis, each pad must acquire at least 5 “good” raster points as deemed by the system software.

How do I access the Assay Design Suite Software?

All of Agena Bioscience’s customers can access the Assay Design Suite online at www.agenacx.com.

Assays by Agena Services

How do you help me design a new assay?

Our Assays by Agena scientists have extensive knowledge and hands-on experience in utilizing the MassARRAY System’s associated products and applications. Assays by Agena services can accommodate your testing needs in the following areas:

  • Genotyping
  • Somatic mutation profiling
  • DNA methylation analysis
  • Quantitative gene expression and copy number variant analysis

Average Turnaround Time: 4-6 weeks.

Will Agena Bioscience help me implement new assays into my routine testing?

Yes. We support our customers with services to validate your new Agena Bioscience test methods with minimal disruption of your routine testing.

Applications and Reagents

What types of applications do you currently support?

Currently we support the following applications:

  • Genotyping, Somatic Mutation, and Quantitative Applications with iPLEX® Reagents
  • Ultrasensitive Somatic Mutation Profiling with UltraSEEK Reagents
  • DNA Methylation Analysis and Pathogen Detection with MassCLEAVE Reagents

Our scientists are always improving our existing chemistry and reagents in order to offer new applications. Make sure to come back often to see the latest updates. Visit our Applications page for more information about the types of reagents that we offer.

How are samples prepared for mass spectrometry?

In order to prepare a sample for the MassARRAY System, laboratories should follow standard endpoint PCR procedures. This includes: DNA extraction, target amplification, extension, and de-salinization before transferring the resulting analyte to the SpectroCHIP Array for use on the MassARRAY Analyzer 4.

Panels

What is the difference between your pre-designed panels and your general reagents?

The pre-designed panels available from Agena Bioscience have been formulated and refined by our research and development organization for a specific purpose. The panels come in ready-to-use kits that can be implemented by your laboratory immediately.

What types of panels do you offer?

We offer a wide variety of ready-to-use panels across several focus areas including: cancer, pharmacogenomics (PGx), blood typing, and sample identification. For more information about all of Agena Bioscience’s panels, visit our panels page.

Cancer

What cancer panels do you offer?

We offer eight cancer panels. They include:

  • UltraSEEK Oncogene Panel v1.0. Screen for 26 somatic mutations in 12 key oncogenes in heterogeneous tumor and blood samples at ≤ 1% frequency.
  • OncoFOCUS Panel v1.0. Screen and confirm over 300 high relevance somatic mutations in EGFR, KRAS, NRAS, and BRAF.
  • OncoCarta Panel v1.0. Screen for 238 somatic mutations across 19 common oncogenes.
  • OncoCarta Panel v2.0. Screen for 152 somatic mutations across 18 cancer genes and tumor suppressors
  • OncoCarta Panel v3.0. Screen for 105 somatic mutations across 22 cancer genes.
  • LungCarta® Panel v1.0. Evaluate 214 somatic mutations in 26 oncogenes and tumor suppressors in non-small cell lung tumors.
  • MelaCarta Panel v1.0. Screen melanoma samples using a targeted discovery panel of more than 70 somatic mutations in 20 genes.
  • GyneCarta Panel v1.0. Screen gynecological tumor samples using a targeted discovery panel of 168 hotspot mutations in 13 genes.
  • LungFUSION Panel. Screen for ALK, RET, or ROS1 translocations in non-small cell lung cancer.
  • ALK Fusion Variant Panel. Screen 11 EML4-ALK and 2 KIF5B-ALK translocations and 2 ALK somatic mutations in non-small cell lung cancer and other cancer types.

For more information about these panels, visit our Cancer Panels page.

What tissue types are compatible with your cancer panels?

The Cancer Panel Collection has been designed for targeted, highly multiplexed analysis for profiling a variety of tumor-derived samples including formalin-fixed tissue, fine needle aspirates, and plasma.

Pharmacogenetics (PGx)

How many Pharmacogenetics panels do you offer?

We currently offer five Pharmacogenetics, or PGx, panels. They include:

  • iPLEX PGx Pro Panel interrogates 191 SNPs in 36 key genes, including CYP2C9, CYP2C19, CYP2D6, and UGT1A1.
  • PGx 68 Panel interrogates 63 SNPs in 16 genes and 5 CNV assays, covering most of the important haplotypes of each gene.
  • CYP2C9 / VKORC1 Panel interrogates 36 SNPs in CYP2C9 and 9 SNPs in VKORC1.
  • CYP2C19 Panel contains assays for 31 SNPs, covering most of the known CYP2C19 haplotypes.
  • CYP2D6 Panel is a set of 30 SNP and 5 CNV assays, covering most of the known CYP2D6 haplotypes.

For more information about these panels, visit our Pharmacogenetics Panels page.

Blood Typing

How many blood group antigen genotyping panels do you offer?

We currently offer a single panel that contains eight distinct modules. The modules include:

  • Hemo ID DQS Module interrogates a variety of markers commonly used for testing donor DNA samples to identify rare donors.
  • Hemo ID Blood Group Genotyping Panel includes all other modules apart from the DQS Module.
  • Hemo ID Kell, Kidd, Duffy Module interrogates genes and variants of the Kell, Kidd and Duffy Systems.
  • Hemo ID MNS Module detects variants of the MNS blood group system.
  • Hemo ID Rare Blood Groups Module detects variants of other systems such as Lutheran, Diego, YT, and many others.
  • Hemo ID RHD-CE Broad Module interrogates genes and variants of the Rhesus blood group system, and includes copy number variation assays for the Rhesus D gene.
  • Hemo ID RHD Variant Module interrogates additional variants in the RHD blood group system.
  • Hemo ID HPA/HNA Module detects human platelet (HPA) and neutrophil (HNA) antigens.

For more information about these panels, visit our Blood Typing Panels page.

Sample ID

How many Sample ID Panels do you offer?

We currently offer two Sample ID Panels. They include:

  • iPLEX Pro Sample ID detects 44 SNPs selected with 45-55% heterozygosity across six major HapMart populations, 3 markers for gender identification, and 5 markers for sample quantification.
  • iPLEX Pro Exome ID detects 44 SNPs, 3 markers for gender identification, and 5 copy number markers in a single multiplexed assay. The copy number markers span a 100-500 bp range to assess potential degradation resulting from sample preparation commonly seen in exome sequencing workflows.

For more information about these panels, visit our Sample ID Panels page.

What tissue types are compatible with your Sample ID Panel?

The Sample ID Panel is compatible with most sample types. The most common samples include:

  • DNA extracted from blood
  • DNA from formalin fixed and frozen tissue samples
  • DNA isolated from blood plasma and serum
  • DNA from FTA cards
  • Whole genome amplified DNA
  • Buccal DNA