Tumor Profiling

The growing number of specialized tumor-profiling tests, and their appetite for formalin-fixed, paraffin embedded (FFPE) tissue, is in direct conflict with the trend towards smaller, less-invasive testing approaches.  Large surgical resections are giving way to core needle biopsies and fine-needle aspirates.  Whereas an FFPE block from a surgical resection may have 250 microns of tissue thickness, core needle biopsies typically have less than 100 microns, and fine needle aspirates even less. Compounding this trend, the needle biopsies are also smaller in cross-sectional area yielding even less tissue per unstained slide.  There simply is not enough tissue for all of the send-out testing.



Several companies are now manufacturing reagents and tests kits that allow local laboratories to offer testing services substantially similar to the offerings by the large centralized laboratories.  As the democratization of tumor profiling is progressed by manufacturers, many laboratories are contemplating, or are already developing, comprehensive approaches that leverage next-generation sequencing to deliver a total and local solution for tumor testing. We believe, however, that several challenges remain for tumor profiling.

Tumor Profiling Challenges

Depletion of available tissue.  Duplicative tissue consumption is not necessarily eliminated by integrating all tumor profiling tests under a single roof.  Distinct sample preparation and testing work streams, each with their own tissue requirements, are the norm in integrated clinical laboratories. As an example of this, consider a laboratory that in-sources all NSCLC testing using IHC for histological subtyping and FDA-approved kits for ALK and EGFR status.  Starting with the tumor block, samples are prepared and sent to distinct laboratory areas:

  • An H&E and at least four unstained slides (TTF-1, P63, and two negative controls) are prepared and sent to the pathologist for review for histological subtyping
  • An H&E and five unstained slides are prepared and sent to the molecular department for EGFR mutation testing
  • An H&E and two unstained slides are prepared and sent to the FISH department for ALK testing

A total of 14 slides, or 70 microns of tissue thickness, are used in this scenario.  If the laboratory is highly efficient it may be able to reduce the number of slides by two or three.  If the sample is very small, however, a choice may have to be made between these tests, all of which have significant therapeutic implications.

Platform proliferation. In the NSCLC example above, three different testing platforms were utilized.  Even if next-generation sequencing is used for EGFR mutation and ALK rearrangement testing, the sample is split into multiple platform workflows:

Testing inefficiencies.  Today, every molecular diagnostic test for FFPE tissue (with the exclusion of FISH) requires extraction of nucleic acids.  Extraction of nucleic acids from FFPE tissue is a multi-step complex technique requiring multiple manual pipetting procedures by highly trained molecular technicians, and several of these manual steps require technician wait time as the samples are being centrifuged or column-separated.  Because the extraction process requires the isolation of nucleic acids from other cellular material, each separation step results in partial specimen loss as well the introduction of biases as the losses are not equal across all nucleic acids being extracted.

The Solution Provided By HTG Molecular

The HTG Edge system platform enables multi-parameter tumor profiling on a single platform from exceedingly small FFPE specimens.

Preservation of precious tumor tissues.  The sample input for sequencing-based HTG assays is a single 5 micron FFPE tissue slide.   

The HTG solution can create opportunities for new treatment approaches in cancers where initial diagnostic biopsies do not yield sufficient tissue for current tumor profiling methods. 


Simple, automated workflow. The HTG EdgeSeq chemistry involves 20 hours of automated sample processing with 2-3 hours of hands-on time for pre- and post- processing.


Dynamic range and scalability of next generation sequencing. NGS based technologies have revolutionized genomics research and molecular diagnostics. By combining the workflow and data quality benefits of HTG assay technology with the power and scale of NGS, HTG is capable of screening 100s – 1000s of genes with a high level of reproducibility.

Learn more about HTG EdgeSeq products and chemistry

HTG EdgeSeq miRNA Expression Profiling
HTG EdgeSeq mRNA Expression Profiling


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

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Last updated: 12/28/2016 - 12:59