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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

Test Codes

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

Department

Molecular Pathology

Specimen Collection Criteria

Collect:

Paraffin-embedded tissue. A paraffin block must be submitted. Submit 10 % formalin-fixed, paraffin-embedded block with corresponding H&E slide. Unstained sections of 5-µm thickness mounted on glass slides can also be used (minimum 5 sections for large tissue and 10 sections for small tissue such as core biopsy). 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/Draw 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

• Tissue decalcified with agents other than Mol Decal (EDTA)  
• Fixatives other than 10% neutral buffered formalin.  
• Improper labeling or inadequate information.   
• Less than 10 percent tumor cellularity
• Poor quality and/or quantity of extracted genomic DNA.  

Testing will be cancelled on specimens meeting the above criteria with client notification. Under certain circumstances (i.e., lack of alternative specimens), testing may proceed with approval from the medical director or designee. 

Inpatient Specimen Preparation

Specimens at Royal Oak may be sent to the Surgical Pathology tube station #201. In-house specimens are also picked up by a Surgical Pathology assistant every hour on the hour. 

In-Lab Processing

Unstained sections of 5-µm thickness are cut from selected tissue blocks. The number of sections cut and the need for macro-dissection are determined by the pathologist, based upon the amount of available tissue and the tumor cellularity. 

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 – Molecular Pathology Laboratory.

Performed

Once or twice per week, dependent upon test volume. 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. See table 1 for the list of genomic regions covered by this test.  
• The test analytical sensitivity is approximately 5% variant in a background of wild-type alleles, with minimum variant coverage of 500x. Variants of lower allele fraction may be detected but may be difficult to distinguish from sequencing errors.  
• 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 benign or likely benign (i.e. unrelated to cancer) may be identified but will not be reported. 
• This test is designed to detect single nucleotide variants (SNVs) and small insertion and deletion mutations of approximate 1-25 bp size (indels). Larger 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.

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). 

Gene coverage is not comprehensive and only regions of particular clinical importance (i.e. hotspots) are included. See table 1 for the list of genomic regions covered by the assay.

Genomic Regions Covered by Trusight Tumor 15 Assay

CPT Codes

81445

Contacts

Last Updated

9/21/2021