Test Overview
Next-Generation Sequencing and Anchored Multiplex Polymerase Chain Reaction (PCR)
Rearrangements resulting in gene fusions are seminal somatic alterations in many solid tumor neoplasms that are often strongly associated with tumor pathogenesis, histopathology, clinical behavior, and response to therapy. In many cases, these gene fusions are disease-defining and essential or supportive for diagnosis, according to diagnostic guidelines including the World Health Organization (WHO) Classification of Tumors; particularly for bone and soft tissue tumors, neuro-oncology tumors, and head and neck tumors. Gene fusions in solid tumors are also important for guiding clinical management, including targeted therapies for specific gene fusions, as well therapeutic determinations based on the diagnosis and prognosis informed by the presence or absence of gene fusions. This assay employs anchored multiplex PCR and next-generation sequencing (NGS) to detect gene fusions involving specific exons within one of the 142 different genes interrogated by this assay (see below).
Interpretive Report Provided
* Reference ranges may change over time. Please refer to the original patient report when evaluating results.
This assay will not detect molecular alterations other than gene fusions and will only detect fusions involving at least one targeted gene region within the defined gene fusion target list, involving the specified exons and with a fusion partner in the designed 5’ or 3’ direction (see below). The panel is designed to detect gene fusions in solid tumors – gene fusions recurrent in hematolymphoid neoplasms are not targeted by this panel.
A negative result does not rule out the presence of a gene fusion not covered by this assay or that is present below the limit of detection of this assay. Because gene fusions are expressed at variable levels, a limit of detection for all gene fusions cannot be determined. The limit of detection for the gene fusions evaluated during validation is 20% fusion-bearing cells. Increased expression of genes not involved in the fusion, e.g. resulting from gene amplification, may also affect the limit of detection.
Rare alterations such as polymorphisms, mutations or fusion breakpoints within or outside of gene-specific primer binding sites may lead to false-negative results. In addition, this assay will only detect gene fusions from rearrangements that result in expressed fusion transcripts (productive rearrangements). This may lead to discrepancies between the results of this testing and gene rearrangement studies in which RNA expression is not evaluated e.g. FISH. This assay may detect one or more transcript(s) resulting from alternate splicing and may lead to a report reflecting an alternate transcript if the longest fusion transcript is not covered by this assay.
Test results should be interpreted in the context of clinical findings, tumor sampling, histopathology, and other laboratory data. If results obtained do not match other clinical or laboratory findings, please contact the laboratory for possible interpretation. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.
Test Details
14-21 days
Specimen Requirements
For formalin-fixed, paraffin-embedded tissue, a block containing an area with a high percentage of neoplastic cells (for micro-/macro-dissection) is preferred. Unstained, UNBAKED slides (5-8, 10-micron slides; 10-15 if few neoplastic cells are present) with associated H&E stained slide are also acceptable. Decalcified tissue or other fixatives will be accepted and the assay attempted, however these may result in failed testing due to degraded nucleic acid. Both blocks and slides should be stored at room temperature. A Diff-Quik or Papanicolaou stained aspirate smear (preferable containing a high percentage and overall amount of neoplastic cells) is also acceptable following digital imaging. Store at room temperature.
Previously extracted RNA may be accepted; however, the extracting laboratory must be CLIA certified and take responsibility for ensuring that viable, neoplastic cells comprise at least 20% of cellularity within the extracted sample.