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Test ID PATH1029 Sanford Solid Tumor NGS Panel, Tumor Cellularity Assessment

Useful For

  • Identifying genomic alterations present in a solid tumor.
  • Determining sensitivity or resistance to a therapeutic agent and eligibility for clinical trials

AKA

SST-NGS; solid tumor profiling; genomic analysis; Sanford solid tumor panel, cellularity assessment (PATH1029); somatic molecular sequencing

Specimen Type/Requirements

  • 1 H&E slide and 10 unstained slides prepared from an FFPE specimen (surgical resection, biopsy, or fine needle aspiration)
    • At least 20% tumor cellularity is required for all FFPE specimens. A pathologist will review slides prior to NGS to determine if the cellularity is adequate.
  • 1 cytology smear slide prepared after a fine needle aspiration (FNA)

Stability/Transport

 Room Temperature  

 Preferred for transport  

* All specimens will be evaluated at the Sanford Medical Genetics Laboratory for test suitability.  Generally, FFPE fixed tissues are stable for several years. However, quality decreases over time with the probability of samples passing from blocks aged roughly 14.5 years is approximately 75%.

Performed Test Frequency

Monday through Friday

Report Available

10-14 days

Additional Information

This test will be ordered as the “Sanford Solid Tumor panel, cellularity assessment” (PATH1029). At the time of ordering, optional immunohistochemistry (IHC) stains may be added on. All FFPE samples will be assessed for tumor cellularity prior to performing the Sanford Solid Tumor NGS (SST-NGS) panel. If a specimen has been determined to be adequate for testing the SST-NGS order (NBLD0705) will be automatically placed.

The optional IHC add-ons are MMR IHC (MLH1, MSH2, MSH6, and PMS2) and PD-L1 IHC (options for SP263 clone, performed at SMC or 22C3 clone sent to Mayo Clinic).

Methodology

Targeted next-generation sequencing (NGS) is performed on the 505 genes listed above. The FDA-cleared PGDx elio™ tissue complete assay is used for library preparation and hybrid capture-based target enrichment, followed by next generation sequencing (NGS) on the Illumina NextSeq 550Dx. The sequence reads are analyzed using FDA-cleared PGDx elio tissue complete bioinformatics pipeline version 1.8.2-4 using human reference genome hg19. This test has been modified to include additional variants, translocations, and amplifications and increase the sensitivity of the assay. The resulting Variant Call Format (VCF) files, tumor mutational burden (TMB) assessment, and microsatellite instability (MSI) status are loaded into QIAGEN Clinical Insight (QCI) Interpret One version 9.3.2 for variant interpretation, clinical assessment, and reporting. TMB is reported as Muts/Mb. MSI status is reported as MSI-high. Single nucleotide variants (SNV), indels, amplifications, and translocations will be reported by this assay.

Performing Lab

Sanford Pathology - Sioux Falls, Fargo, Bismarck, Bemidji

Sanford Medical Genetics Laboratory, Sioux Falls

CPT

88358 – tumor cellularity assessment

81455 – NGS

88360 – optional add-on PD-L1 IHC

88341 – optional add-on MLH1, MSH2, MSH6 IHC

88342 – optional add-on PMS2 IHC

Limitations

Performance specifications have been established for the FDA-cleared PGDx elio tissue complete. This assay is not designed to be used as a standalone assessment for treatment decision or patient care. Treatment decisions and patient care should be based on the treating physician’s medical judgement, taking into consideration all applicable information concerning the patient's condition, consistent with standard of care. The clinical validity of this test for predicting treatment effect has not been established. 

 

The assay was validated using samples with a minimum of 20% tumor cells in the tissue area extracted. Rare and novel germline variants not listed in population databases may be reported and cannot be distinguished from somatic variants. This assay may not detect all instances of contamination, particularly when adjacent samples are from individuals of the same ancestry. If indicated, testing with an FDA-approved companion diagnostic should be performed to assess patients for selection of therapy. Decalcified bone specimens are not an acceptable specimen type.

 

As with all somatic assays, tumor heterogeneity contributes to variance between assays due to sampling bias. A negative result does not rule out the presence of a mutation below the Limit of Detection (LOD) of the assay.