Next generation sequencing of amplification products are performed on the Ion Torrent Personal Genome Machine and analyzed with the Torrent Suite Software. Reference DNA sequences used for these genes can be found at hhtp://www.ncbi.nlm.nih.gov/refseq/rsg/. This mutation panel is designed to detect targeted mutations only. Confirmation of these mutations is performed by traditional or real time PCR followed by Sanger sequencing, fluorescent melting curve analysis and/or pyrosequencing.

Extracted nucleic acid specimens may occasionally be received in cases where no primary sample is available for testing.  All nucleic acid specimens received for testing must have been extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS.

Batched runs begin on Monday or first working day of each week and Wednesday of each week.

FFPE tissue - The percentage of tumor in the specimen should be ≥20%. Specimens with <20% tumor will be evaluated on a case by case basis to determine whether macro-dissection is possible based on the dispersal of cells.

A documented prior authorization will need to be present in Health Link before testing can be performed. 

The ordering source should consult the Genetic Testing at UW Health Clinical Laboratories document on U-Connect prior to ordering testing. Contact UWHC Referral office at (608) 262-6388 for questions. 

Three slides each containing 5 microns (uM) of FFPE tissue should be sent. Second slide should be H&E stained with the tumor circled. Please indicate percent tumor on the H&E.

 

In order to ensure that molecular testing is conducted on a representative sample and a direct correlation of molecular results with morphologic findings is possible, a pathologist selects the specimen(s) and, whenever possible, identifies the suspicious or neoplastic cells submitted for molecular testing.

Transport with a cold pack. Avoid excessive heat.

Transport at room temperature or with a cold pack. Avoid excessive heat.

Specimens processed in alternative fixatives 

A written interpretive report is provided by the laboratory detailing all genetic variants detected and genes in the panel. The significance of genetic variants to pathogenicity and therapeutic response will be indicated whenever possible.

Inadequate specimen collection, processing and storage may invalidate test results.

A "Not Detected" result may be due to either insufficient tissue or tumor present in the sample, tumor heterogeneity, to the presence of inhibitors or to bias or inefficiencies in PCR amplification. The four genes covered are not all sequenced in their entirety. Mutations outside the amplicons will not be detected. The limit of detection of this assay is estimated to be 5% at 500X coverage and 10% at 200X coverage and mutations below 100X coverage cannot reliably be detected. This technology cannot detect large insertions, deletions, duplications or genomic copy number variants. Rare or complex polymorphisms may be present that could lead to false negative or positive results.

This test cannot differentiate between somatic or germline genetic variants. Additional testing may be necessary to clarify the significance of results if there is a potential for hereditary risk. It is recommended that patients receive genetic consultation where appropriate, to explain the implications of this test result, including probabilistic risk of disease and uncertainties, and the reproductive or medical options it raises.  Test results should be interpreted in the context of clinical findings, tumor sampling, histopathology, and all other laboratory data. The presence or absence of cancer associated mutations does not guarantee either a positive or negative response to therapy.

All test results should be interpreted in the context of patient's clinical presentation.

A "Detected" results indicates the presence of a variant. This test should not be used as the only criterion to form a clinical conclusion, instead, results should be correlated with other test results, patient symptoms and clinical presentation.

The variants nomenclature used is recommended by the Human Genome Variation Society (http://www.hgvs.org/mutnomen/).

The performance characteristics of this test were validated by UWHC Clinical Laboratories. The U.S. Food and Drug Administration (FDA) has not approved or cleared this test; however, FDA approval or clearance is currently not required for clinical use of this test. The UWHC Clinical Laboratories is authorized under Clinical Laboratory Improvement Amendments (CLIA) to perform high-complexity testing.

A professional fee is associated with this test (CPT Code G0452).