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Dec 8, 2017

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Lung Cancer (EGFR, KRAS, BRAF, ERBB) Mutation Panel by Next Generation Sequencing

Lung Cancer (EGFR, KRAS, BRAF, ERBB) Mutation Panel by Next Generation Sequencing (HCLCMP) Molecular Diagnostics Lab Test

Name: Lung Cancer (EGFR, KRAS, BRAF, ERBB) Mutation Panel

Test Name: Lung Cancer (EGFR, KRAS, BRAF, ERBB) Mutation Panel by Next Generation Sequencing

Health Link Test Code: HCLCMP

LIS Test Code: LCMP

CPT Code(s): 81210 (BRAF), 81275 (KRAS codons 12 and 13 in exon 2), 81276 (KRAS codon 61 in exon 3), 81235 (EGFR), 81479 (ERBB2)

Test Component:

This discrete Lung Cancer Mutation Panel used targeted next-generation sequencing to evaluate for somatic mutations within the BRAF, KRAS, EGFR and ERBB2 genes. 

 

Refer to Mutation List on U-Connect for complete list of somatic mutations for each of these gene.

Methodology: Next Generation Sequencing

Clinical Information:

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.

Days Performed: Once a week.

In-Lab Turnaround Time: 2 weeks.

Specimen: Formalin-fixed, paraffin embedded tissue, whole blood or bone marrow aspirate

Collection Container: Lavender top

Collection Instructions:

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

 

Provider must contact patient’s insurance about coverage for this molecular test and then counsel the patient on out-of-pocket costs.

 

For Unity and WI-MA patients, documented prior authorization will need to be present in Health Link or sent to laboratory before test will be collected and/or performed.

 

For all other managed care plans, referral must be placed in Health Link in order for testing on tissue or bone marrow specimens to be performed at UW Health; and patients should be referred to their primary care physician for collection of blood specimens.

 

For any other insurers, providers must check with insurer before ordering testing.

Collection Volume: 1 mL

Pediatric Collection Volume: 0.6 mL

Stability Ambient:

Indefinitely.

Stability Refridgerated:

Indefinitely.

Stability Frozen:

Not acceptable.

Sample Analyzed: Tissue, whole blood, or bone marrow

Testing Volume: 1 mL

Pediatric Testing Volume: 0.6 mL

Specimen Processing:

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 Intra-Lab Send-Out Form.

Blood/Bone Marrow Aspirate - Whole Blood. Do not centrifuge.

 

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.

Outreach Specimen Processing:

Transport with a cold pack. Avoid excessive heat.

Specimen Transport:

Transport at room temperature.

Interpretation:

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.

Test Limitations:

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. 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.

Additional Information:

A "Detected" results indicates the presence of a variant. Inadequate specimen collection, processing and storage may invalidate test results. 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).