Test Catalog

Test Id : LNGPR

Lung Cancer-Targeted Gene Panel with Rearrangement, Tumor

Useful For
Suggests clinical disorders or settings where the test may be helpful

Identifying lung tumors that may respond to targeted therapies by assessing multiple gene targets simultaneously in EGFR, BRAF, KRAS, HRAS, NRAS, ALK, ERBB2, MET, ALK, ROS1, RET, and NTRK1 genes

 

Diagnosis and management of patients with lung cancer

 

This test is not intended for use for hematological malignancies.

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test uses targeted next-generation sequencing to evaluate for somatic mutations within the EGFR, BRAF, KRAS, HRAS, NRAS, ALK, ERBB2, and MET genes. Next-generation sequencing is also used to identify rearrangements (fusions) involving ALK, ROS1, RET, and NTRK1. See Targeted Gene Regions Interrogated by Lung Panel and Activated/Partner Gene Breakpoints Resulting in Targeted Fusion Transcripts Interrogated by Lung Panel for details regarding the targeted gene regions evaluated by this test.

 

Of note, this test is performed to evaluate for somatic mutations and rearrangements (fusions) within solid tumor samples. This test is not intended for use for hematological malignancies. Additionally, this test does not assess for germline alterations within the genes listed.

 

This test identifies activating exon 14 skipping mutations in MET.

Highlights

Evaluates formalin-fixed, paraffin-embedded tumor or cytology slides from patients with lung cancer for gene mutations and rearrangements (fusions) to identify candidates for targeted therapy.

 

Current data suggests that the efficacy of EGFR-targeted therapies in patients with non-small cell lung cancer is limited to tumors with mutations in the EGFR gene.

 

Current data suggests that lung carcinomas with ALK rearrangements may be sensitive to ALK inhibitors.

Additional Tests
Lists tests that are always performed, at an additional charge, with the initial tests.

Test Id Reporting Name Available Separately Always Performed
SLIRV Slide Review in MG No, (Bill Only) Yes

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

When this test is ordered, slide review will always be performed at an additional charge.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Polymerase Chain Reaction (PCR)-Based Next Generation Sequencing

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Lung Panel with Rearrangement Tumor

Aliases
Lists additional common names for a test, as an aid in searching

EGFR

BRAF

KRAS

HRAS

NRAS

ERBB2

MET

ALK

ROS1

RET

NTRK1

Lung cancer panel

Lung cancer rearrangement

Lung cancer fusion

Lung panel

Lung tumor panel

Tumor panel

Oncology panel

Next Gen Sequencing Test

NGS

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

When this test is ordered, slide review will always be performed at an additional charge.

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

Multiple oncology (cancer) gene panels are available. For more information see Oncology Somatic NGS Testing Guide.

Necessary Information

Pathology report (final or preliminary) at minimum containing the following information must accompany specimen in order for testing to be performed:

1. Patient name

2. Block number-must be on all blocks, slides and paperwork (can be handwritten on the paperwork)

3. Tissue collection date

4. Source of the tissue

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

This assay requires at least 20% tumor nuclei.

-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue144 mm(2)

-Minimum amount of tumor area: tissue 36 mm(2)

-These amounts are cumulative over up to 10 unstained slides and must have adequate percent tumor nuclei.

-Tissue fixation: 10% neutral buffered formalin, not decalcified

-For specimen preparation guidance, see Tissue Requirement for Solid Tumor Next-Generation Sequencing. In this document, the sizes are given as 4mm x 4mm x 10 slides as preferred: approximate/equivalent to 144 mm(2) and the minimum as 3mm x 1mm x 10 slides: approximate/equivalent to 36mm(2).

 

Preferred:

Specimen Type: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block with acceptable amount of tumor tissue.

 

Acceptable:

Specimen Type: Tissue slide

Slides: 1 stained and 10 unstained

Collection Instructions: Submit 1 slide stained with hematoxylin and eosin and 10 unstained, nonbaked slides with 5-micron thick sections of the tumor tissue.

Note: The total amount of required tumor nuclei can be obtained by scraping up to 10 slides from the same block.

Specimen Type: Cytology slide (direct smears or ThinPrep)

Slides: 1 to 3 slides

Collection Instructions: Submit 1 to 3 slides stained and cover slipped with a preferred total of 5000 nucleated cells or a minimum of at least 3000 nucleated cells.

Note: Glass coverslips are preferred; plastic coverslips are acceptable but will result in longer turnaround times.

Additional Information: Cytology slides will not be returned.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

See Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Other Specimens that have been decalcified (all methods) Specimens that have not been formalin-fixed, paraffin-embedded

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
Frozen
Refrigerated

Useful For
Suggests clinical disorders or settings where the test may be helpful

Identifying lung tumors that may respond to targeted therapies by assessing multiple gene targets simultaneously in EGFR, BRAF, KRAS, HRAS, NRAS, ALK, ERBB2, MET, ALK, ROS1, RET, and NTRK1 genes

 

Diagnosis and management of patients with lung cancer

 

This test is not intended for use for hematological malignancies.

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test uses targeted next-generation sequencing to evaluate for somatic mutations within the EGFR, BRAF, KRAS, HRAS, NRAS, ALK, ERBB2, and MET genes. Next-generation sequencing is also used to identify rearrangements (fusions) involving ALK, ROS1, RET, and NTRK1. See Targeted Gene Regions Interrogated by Lung Panel and Activated/Partner Gene Breakpoints Resulting in Targeted Fusion Transcripts Interrogated by Lung Panel for details regarding the targeted gene regions evaluated by this test.

 

Of note, this test is performed to evaluate for somatic mutations and rearrangements (fusions) within solid tumor samples. This test is not intended for use for hematological malignancies. Additionally, this test does not assess for germline alterations within the genes listed.

 

This test identifies activating exon 14 skipping mutations in MET.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

When this test is ordered, slide review will always be performed at an additional charge.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Targeted cancer therapies are defined as antibody or small molecule drugs that block the growth and spread of cancer by interfering with specific cell molecules involved in tumor growth and progression. Multiple targeted therapies have been approved by the FDA for treatment of specific cancers. Molecular genetic profiling is often needed to identify targets amenable to targeted therapies and to minimize treatment costs and therapy-associated risks.

 

Next-generation sequencing has recently emerged as an accurate, cost-effective method to identify alterations across numerous genes known to be associated with response or resistance to specific targeted therapies. This is a single assay that uses formalin-fixed paraffin-embedded tissue or cytology slides to assess for common somatic mutations and rearrangements (fusions) involving 11 genes known to be associated with lung cancer. The results of this test can be useful for assessing prognosis and guiding treatment of individuals with lung tumors. These data can also be used to help determine clinical trial eligibility for patients with alterations in genes not amenable to current FDA-approved targeted therapies.

 

See Targeted Gene Regions Interrogated by Lung Panel and Activated/Partner Gene Breakpoints Resulting in Targeted Fusion Transcripts Interrogated by Lung Panel for details regarding the targeted gene regions evaluated by this test.

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretative report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

An interpretive report will be provided.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

This test cannot differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.

 

DNA variants of uncertain significance may be identified.

 

A negative (wild-type) result does not rule out the presence of a mutation or rearrangement (fusion) that may be present but below the limits of detection of this assay.

 

Point mutations and small insertion/deletion mutations will be detected in the EGFR, BRAF, KRAS, HRAS, NRAS, ERBB2, ALK and MET genes only. Gene rearrangements (fusions) involving ALK, ROS1, RET and NTRK1 genes only will be detected. This test does not detect large single or multiexon deletions or duplications or genomic copy number variants in any of the genes tested.

 

Rare polymorphisms may be present that could lead to false-negative or false-positive results. 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 for updated interpretation. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

Reliable results are dependent on adequate specimen collection and processing. This test has been validated on cytology slides and formalin-fixed, paraffin-embedded tissues; other types of fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause PCR failure.

Supportive Data

We have developed a next generation sequencing assay to detect somatic mutations and gene rearrangements (fusions) that can be used to assist in predicting prognosis and identifying targeted therapies for the management of patients with lung cancer. This assay has been shown to be very reproducible, having a 100% concordance for intra- and interassay reproducibility experiments.

 

Detection of Somatic Mutations (DNA)

We observed 96.2% concordance, detecting 75 of 78 somatic mutations that had previously been detected by various other molecular methods. These mutations included 61 SNPs and 17 Indels across ALK (n=3), BRAF (n=15), EGFR (n=17), ERBB2 (n=7), HRAS (n=2), KRAS (n=17), MET (n=5), and NRAS (n=12) genes in 70 known unique samples. No pathogenic variants were detected in the 29 unique, known mutation negative samples.

 

Detection of Fusion Transcripts (RNA)

We observed 100% concordance, detecting rearrangements resulting in fusion transcripts in 26 of 26 unique samples with previously detected by fluorescent in situ hybridization (FISH) or another sequencing assay. These rearrangements involved the ALK (n=19), ROS1 (n=3), and RET (n=4) genes. No fusion transcripts were detected in 72 unique samples that had mutually exclusive mutations or were negative for rearrangements as assessed by standard FISH analysis.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Beadling C, Neff TL, Heinrich MC, et al: Combining highly multiplexed PCR with semiconductor-based sequencing for rapid cancer genotyping. J Mol Diagn 2013;15:171-176

2. Sharma SV, Bell DW, Settleman J, Haber DA: Epidermal growth factor receptor mutations in lung cancer. Nat Rev Cancer 2007;7(3):169-181

3. Mok TS: Personalized medicine in lung cancer: What we need to know. Nat Rev Clin Oncol 2011;8:661-668

4. Cheng L, Alexander RE, Maclennan GT, et al: Molecular pathology of lung cancer: key to personalized medicine. Mod Path 2012;25(3):346-369

5. Shigematsu H, Gazdar AF: Somatic mutations of epidermal growth factor receptor signaling pathway in lung cancers. 2006 Jan 15;118(2):257-262

6. Gao G, Ren S, Li A, et al: Epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) therapy is effective as first-line treatment of advanced non-small-cell lung cancer with mutated EGFR: a meta-analysis from 6 phase III randomized controlled trials. Int J Cancer 2012 Sep 1;131(5):E822-829

7. Takeuchi K, Soda M, Togashi Y, et al: RET, ROS1 and ALK fusions in lung cancer. Nat Med 2012;18(3):378-381

8. Eberhard DA, Johnson BE, Amler LC, et al: Mutations in the epidermal growth factor receptor and in KRAS are predictive and prognostic indicators in patients with non-small-cell lung cancer treated with chemotherapy alone and in combination with erlotinib. J Clin Oncol 2005;23(25):5900-5909

9. Frampton GM, Ali SM, Rosenzweig M, et al: Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors. Cancer Discov 2015 Aug 5(8):850-859

10. Vaishnavi A, Capelletti M, Le AT, et al: Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer. Nat Med. 2013 Nov;19(11):1469-1472

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Next-generation sequencing (NGS) is performed to test for the presence of a mutation in targeted regions of the EGFR, BRAF, KRAS, HRAS, NRAS, ALK, ERBB2, and MET genes. NGS is performed to test for the presence of rearrangements involving the ALK, ROS1, RET, and NTRK1 genes. See Targeted Gene Regions Interrogated by Lung Panel and Activated/Partner Gene Breakpoints Resulting in Targeted Fusion Transcripts Interrogated by Lung Panel for details regarding the targeted gene regions evaluated by this test.(Unpublished Mayo method)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Monday through Friday

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

12 to 20 days

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

81445-Targeted genomic sequence analysis panel, solid organ neoplasm

Slide Review

88381-Microdissection, manual

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
LNGPR Lung Panel with Rearrangement Tumor In Process
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
44143 Result Summary 50397-9
44144 Result 82939-0
44145 Interpretation 69047-9
44146 Additional Information 48767-8
44147 Specimen 31208-2
44148 Source 31208-2
46912 Tissue ID 80398-1
44149 Released By 18771-6

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports

Test Update Resources

Change Type Effective Date
Obsolete Test 2022-10-24