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Specimen-to-variant report NGS automation in a single day for inherited disease applications

Since 2011, Ion Torrent next-generation sequencing (NGS) has provided complete solutions for clinical research of human diseases with leading Ion AmpliSeq technology.

Now, Ion AmpliSeq On-Demand Panels are available for the Ion Torrent Genexus System. Together, they provide a powerful targeted NGS workflow that enables any lab to go from specimen to variant report in a single day*, providing accessibility, efficiency, and convenience at a speed never possible before.

This highly flexible system lets you process samples—even just one—cost-effectively, as they come in. The hands-off, set-up-and-go workflow makes NGS accessible, even if your human genetics lab is new to the technology.

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In-house NGS accessible like never before

Ion Torrent NGS reduces complexities that come with other sequencing methods

Dr. Jose Costa, Affiliate Researcher at IPATIMUP, discusses how Ion Torrent NGS enables clinical research labs to overcome common challenges of bringing NGS to their lab.

See how IPATIMUP is developing targeted NGS assays for the Genexus system and Ion GeneStudio S5 system to further clinical research into Noonan syndrome and other RASopathies. Read blog post >

Watch presentation: Rapid RASopathies testing using custom Ion AmpliSeq Panel with Ion Torrent Genexus System ›

Benefits of Ion AmpliSeq On-Demand Panels on the Genexus System for inherited disease clinical research:

  • Unprecedented specimen-to-variant report automation and ease of use—just 10 minutes of hands-on time and two user touchpoints
  • Single-day turnaround time—from biological specimen to variant report*
  • Easy panel design iteration—built with leading amplicon-based enrichment technology for targeted sequencing, Ion AmpliSeq On-Demand panels are customizable targeted NGS panels with pretested genes for germline diseases like hereditary cancer

Experience unprecedented specimen-to-variant report automation in a single day*

The Ion Torrent Genexus System integrates and automates nucleic acid extraction and purification, library preparation, sequencing, and analysis under a single software ecosystem. This all-in-one solution boosts your lab’s overall efficiency by reducing the number of instruments and consumables required in the lab and frees up your time for more technical applications.

With just 10 minutes of hands-on time and two touchpoints, all users can get up and running quickly with significantly less training, making NGS accessible even if your lab is new to the technology.

Genexus System workflow for inherited disease clinical research applications

How the Genexus System workflow stacks up

Genexus System workflow touchpoints and hands-on time

Design with confidence—gene panels on demand, how and when you want them

Ion AmpliSeq On-Demand Panels enables flexible design and iteration of custom gene panels for clinical research of human diseases—conveniently and with confidence.

Convenient and robust gene selection tool


Our powerful content selection engine automates optimal gene selection based on the degree of gene/disease association, informed by public databases like MeSH.

Proceed with confidence


Over 5,000 genes available in the selection tool are optimized and pretested, with wet-lab performance data, allowing you to proceed with confidence in your panel design and clinical research outcomes.

Flexible panel design with catalog of over 5,000 pretested genes

Easily configure your panel from an optimized catalog of over 5,000 wet-lab tested genes most relevant in clinical research of inherited diseases like hereditary cancers, primary immunodeficiency, hearing loss, muscular dystrophy, Noonan syndrome and many more (Figure 1).

Featured clinical research application—hereditary cancer genomics (CGx)


There’s no time to waste. With just 10 minutes of hands-on time and two user touchpoints, our solution for clinical research of hereditary cancer enables single-day turnaround time from biological specimen to variants*.

Leverage the power of automation, rapid turnaround time, and easy NGS panel design with the winning combination of Genexus System and Ion AmpliSeq On-Demand Panels—an optimal pairing for studying hereditary cancers.

Application note: Identification of relevant genetic variants in hereditary cancer research samples


In this application note, we demonstrate the DNA-to-variant report NGS workflow on the Genexus Integrated Sequencer using two Ion AmpliSeq On-Demand panels for clinical research of hereditary cancer.

See the performance data ›

Pretested genes for common hereditary cancer clinical research applications are available for Ion AmpliSeq On-Demand panels

Tumor typeGenes
BreastBRCA1, BRCA2
Basal cell carcinomaPTCH1, PTCH2, SUFU
Endocrine glandCDKN1B, MEN1, NTRK1, RET
KidneyDIS3L2, POU6F2, VHL, WT1
Connective and soft tissueEXT1, EXT2, LIFR, PTH1R, PTPN11
Nervous systemLZTR1, NF1, NF2, SMARCB1
OvarianBRCA1, BRCA2
SkinMLH1, MSH2

Ion AmpliSeq On-Demand Panel design and ordering

  1. Visit the Ion AmpliSeq Designer at and sign in. If you do not have an account, follow the registration process to create a new account. There are no costs associated with creating an account.
  2. After signing in, locate “Ion AmpliSeq On-Demand Panels” on the homepage.
  3. Start a design by browsing the disease research areas (Figure 2) or input your own gene list.

If you don’t see all of your genes of interest listed within our catalog, you can still design an Ion AmpliSeq On-Demand Panel with additional genes spiked-in.

Or create a fully custom gene panels with Ion AmpliSeq Made-to-Order Panels.
Contact your sales representative for ordering support.

Genexus Integrated Sequencer ordering information

Please fill out the project request form to inquire about ordering the Genexus Integrated Sequencer for inherited disease clinical research applications.


* Specimen-to-variant report workflow will be available after the Ion Torrent Genexus Purification System and integrated reporting capabilities are added in 2020.

For Research Use Only. Not for use in diagnostic procedures.