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Beaumont Laboratory

Solid Tumor 15 Genes Panel by NGS

Solid Tumor Mutation Panel by Next Generation Sequencing, NGS, Next Generation Sequencing, Solid Tumor Panel. Illumina, MiSeq, Colon Cancer, Lung Cancer, Melanoma, Gastrointestinal Stromal Tumor, SOFTPATH: TST15, SOFT MOL: TST15, SOFT LAB: TST15

Specimen Collection Criteria

Collect:

Paraffin-embedded tissue. A paraffin block must be submitted. (Slides or paraffin shavings are not acceptable.) Submit 10 % formalin-fixed, paraffin-embedded block with corresponding H&E slide. Tissue should be well fixed and well processed. Average tissue size 5.0 mm2.

  • DNA will be assessed for quality. If it is deemed unacceptable, testing will be cancelled with client notification.
  • The specimen must be accompanied by a completed requisition and must contain the patient name, date of birth, collection date, ordering physician, and source of specimen.

Physician Office/Drawsite Specimen Preparation

Maintain paraffin-embedded tissue at room temperature (20-26°C or 68-78.8°F) until transport.

Preparation for Courier Transport

Transport: Paraffin-embedded tissue or slides, at room temperature (20-26°C or 68-78.8°F).

Rejection Criteria

  • Decalcified tissue.
  • Fixatives other than 10% neutral buffered formalin.
  • Specimens fixed/processed in alternative fixatives (e.g. alcohol, zinc formalin).
  • Improper labeling or inadequate information. 
  • Less than 10 percent tumor cellularity, at discretion of medical director.
  • Poor quality and/or quantity of extracted genomic DNA.

Testing will be cancelled on specimens meeting the above criteria with client notification.

Storage

Specimen Stability for Testing:

Room Temperature (20-26°C or 68-78.8°F): Indefinitely
Refrigerated (2-8°C or 36-46°F): Unacceptable
Frozen (-20°C/-4°F or below): Unacceptable

Specimen Storage in Department Prior to Disposal:

Room Temperature (20-26°C or 68-78.8°F): 7 days

Specimen Storage (DNA libraries post testing):

Frozen (-25 to -15°C): 2 months

Laboratory

Royal Oak Anatomic Pathology - Advanced Diagnostics Laboratory.

Performed

Once per week, usually Monday.
Results available in 10-15 business days.

Reference Range

No variants detected or only likely benign variants detected.

Test Methodology

Tissue sections are reviewed by a pathologist and relevant tumor is selected for analysis. DNA is isolated from the sample and quantified. The DNA isolates are prepared for sequencing with the Illumina TruSight Tumor 15 library preparation kit and sequenced on the Illumina MiSeq instrument with the Illumina TruSight Tumor 15 sequencing kit. Analysis is performed with MiSeq Reporter and Cartagenia BenchLab. A personalized interpretive report is generated for each sample that lists the variants detected in each gene, classifies these based on a standardized classification scheme for somatic variants, and provides detailed interpretative comments for each variant.

 

Test Limitations:

  • The content of this test is not optimized for tumor types other than those listed (e.g. leukemia, lymphoma, sarcomas other than GIST).
  • This test is designed to detect somatic variants only. The status of potential germline variants cannot be verified because parallel testing is not performed on paired normal tissues. Additional testing is necessary for any potential hereditary risk.
  • Variants occurring in the listed genes but outside of the targeted regions will not be detected by this assay.
  • The test analytical sensitivity is approximately 5% variant in a background of wild-type alleles, with minimum variant coverage of 500x.
  • Rare false positives and negatives may occur due to errors in sequencing chemistry. Quality assurance criteria are established to minimize such occurrences.
  • Variants which are present in the targeted area but with allele frequencies below the established analytical sensitivity will not be detected by this assay.
  • Germline variants that are frequent in the general population and considered unrelated to cancer may be identified but will not be reported. A list of such variants commonly seen in this assay will be maintained and made available for client reference.
  • This test is designed to detect single nucleotide variants (SNVs) and small insertion and deletion mutations of approximate 1-25 bp size (indels). Large insertions and deletions, copy number changes, and genomic rearrangements will not be detected by this assay.
  • Variant interpretations are based upon data from public databases available at the time of case sign out and do not reflect new information that becomes available after that date.

 

Test results should be interpreted in the context of clinical findings, tumor sampling and other laboratory data. If results obtained do not match other clinical or laboratory findings, please contact the laboratory director(s) for updated interpretation.

Clinical Utility

This test is intended to detect somatic mutations of the AKT1, BRAF, EGFR, ERBB2, FOXL2, GNA11, GRAQ, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, RET, and TP53 genes that have established prognostic and predictive relevance for therapeutic purposes. Research into useful biomarkers for solid tumors is progressing rapidly and multiple established and investigational genetic targets now exist for several tumor types. Given these advances in knowledge, it has now become desirable to test multiple genetic targets in parallel on a single sample. This assay is performed with next generation sequencing methodology that tests for mutations in all 15 panel genes simultaneously on a single DNA sample. This methodology allows for greatly improved throughput and utility of limited samples compared to the performance of multiple traditional single-gene tests such as allele-specific PCR and Sanger sequencing. Clinically relevant tumor panels that can be reported by this assay include the following:  Lung adenocarcinoma (EGFR, KRAS, BRAF, ERBB2, MET, and RET), Colorectal adenocarcinoma (KRAS, NRAS, BRAF, and PIK3CA), Melanoma (BRAF, KIT, NRAS, and GNAQ), and Gastrointestinal Stromal Tumor (KIT and PDGFRA).

CPT Code

81445.

Test Codes

SOFTPATH: TST15, SOFT MOL: TST15, SOFT LAB: TST15

Last Updated

10/17/2017

Microtainer® and Vacutainer® are registered trademarks of Becton, Dickinson and Company.
UroVysion® is a registered trademark of Abbott Laboratories. ThinPrep® is a registered trademark of Hologic, Incorporated.

This directory currently reflects information only for specimens collected and/or processed at the Farmington Hills, Grosse Pointe, Royal Oak, and Troy campuses.