Test Catalog

Test Id : MCLNR

MayoComplete Lung Rearrangements, Rapid, Tumor

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

Identifying lung tumors that may respond to targeted therapies by simultaneously assessing multiple genes involved in rearrangements resulting in fusion transcripts

 

Diagnosis and management of patients with lung cancer

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

This test identifies specific gene fusions (rearrangements) involving the ALK, ROS1, and RET genes, MET exon 14 skipping, and expression imbalance for ALK, ROS1, RET, NTRK1, NTRK2, and NTRK3 genes. See Targeted Genes and Methodology Details for MayoComplete Lung Rearrangements for details regarding the targeted gene regions evaluated by this test.

 

Expression imbalance assays have the benefit that provide an indication of the presence of a fusion not covered by the specific fusion panel.

 

This test is performed to evaluate gene fusions (rearrangements) within solid tumor, in particular lung cancer, specimens.

Highlights

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

 

Current data suggests that lung carcinomas with ALK, ROS1, RET rearrangements and MET exon 14 skipping may be sensitive to corresponding tyrosine kinase inhibitors.

 

Current data suggests that solid tumors with NTRK rearrangements may be sensitive to multikinase 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 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)

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

No

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

MayoComplete Lung Rearrangements

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

ALK

Lung cancer fusion

Lung cancer rearrangement

MET exon 14

NTRK1

NTRK2

NTRK3

RET

ROS1

Mayo Complete

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 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 10% tumor nuclei.

-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue 36 mm(2)

-Minimum amount of tumor area: tissue 18 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

 

Preferred:

Specimen Type: Tissue block and cell block

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

 

Acceptable

Specimen Type: Tissue slides

Slides: 1 Stained and 5 unstained

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

Note: The total amount of required tumor nuclei can be obtained by scraping up to 5 slides from the same block.

Additional Information: Unused unstained slides will not be returned.

 

Specimen Type: Cytology slides (direct smears)

Slides: 1 to 3 Slides for smears

Collection Instructions: Submit 1 to 3 slides unstained or stained with Diff Quik or Pap 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 used in testing will have everything scraped and not be returned.

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

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

Specimens that have been decalcified (all methods)
Specimens that have not been formalin fixed, paraffin-embedded, except for cytology slides
Extracted nucleic acid (DNA or RNA)
Reject

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)
Refrigerated

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

Identifying lung tumors that may respond to targeted therapies by simultaneously assessing multiple genes involved in rearrangements resulting in fusion transcripts

 

Diagnosis and management of patients with lung cancer

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

This test identifies specific gene fusions (rearrangements) involving the ALK, ROS1, and RET genes, MET exon 14 skipping, and expression imbalance for ALK, ROS1, RET, NTRK1, NTRK2, and NTRK3 genes. See Targeted Genes and Methodology Details for MayoComplete Lung Rearrangements for details regarding the targeted gene regions evaluated by this test.

 

Expression imbalance assays have the benefit that provide an indication of the presence of a fusion not covered by the specific fusion panel.

 

This test is performed to evaluate gene fusions (rearrangements) within solid tumor, in particular lung cancer, specimens.

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 US Food and Drug Administration (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.

 

Fusions involving the NTRK1, NTRK2, or NTRK3 genes (ie, NTRK gene fusions) form through intra- and interchromosomal rearrangements. NTRK gene fusions lead to activation of downstream MAPK, PIK, and STAT3 signaling pathways and act as oncogenic drivers of multiple types of pediatric and adult solid tumors. In solid tumors, the presence of an NTRK gene fusion is a biomarker for response to tropomyosin receptor kinase inhibitor therapy.

 

Lung cancers harboring ALK rearrangements are resistant to epidermal growth factor receptor tyrosine kinase inhibitors, but may be highly sensitive to ALK inhibitors, like Xalkori (crizotinib). The drug Xalkori works by blocking certain kinases, including those produced by the abnormal ALK gene. Clinical studies have demonstrated that Xalkori treatment of patients with tumors exhibiting ALK rearrangements can halt tumor progression or result in tumor regression.

 

RET rearrangements occur in approximately 2.5% to 10% of sporadic papillary thyroid cancer(1) and 1% to 3% of non-small cell lung cancer. The most prevalent fusions are KIF5B exon 15 - RET exon 12 and KIF5B exon 16 - RET exon 12, which represent over 75% of RET fusions.

 

ROS1 (c-ros oncogene 1), originally described in glioblastomas, has been identified as a potential relevant therapeutic target in lung adenocarcinoma. Crizotinib has shown in vitro activity and early evidence of clinical activity in ROS1-rearranged tumors.

 

Many cases of METex14 alterations are found in lung adenocarcinomas, these events have a much higher incidence in pulmonary sarcomatoid carcinomas. Approximately 20% to 30% of sarcomatoid carcinomas harbor METex14 alterations.

 

See Targeted Genes and Methodology Details for MayoComplete Lung Rearrangements

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 interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

The interpretation of molecular biomarker analysis includes an overview of the results and the associated diagnostic, prognostic, and therapeutic implications.

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.

 

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

 

Gene fusions (rearrangements) and expression imbalance involving the ALK, ROS1, RET, NTRK1, NTRK2, and NTRK3 genes only will be detected. This test does not detect point mutations, insertion/deletion mutations, large single or multiexon deletions or duplications, or genomic copy number variants in any of the genes tested.

 

Rare alterations (ie, polymorphisms) may be present that could lead to false-negative or false-positive results.

 

The presence or absence of a variant may not be predictive of response to therapy in all patients.

 

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 polymerase chain reaction failure.

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

1. 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

2. US Food and Drug Administration (FDA): Table of Pharmacogenomic Biomarkers in Drug Labeling. FDA; Updated March 29, 2022, Accessed August 3, 2022. Available at www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling

3. Shaw AT, Kim DW, Nakagawa K, Seto T, Crino L, Ahn MJ, et al. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med. 2013;368(25):2385-94. doi: 10.1056/NEJMoa1214886.

4. Sehgal K, Patell R, Rangachari D, Costa DB. Targeting ROS1 rearrangements in non-small cell lung cancer with crizotinib and other kinase inhibitors. Transl Cancer Res. 2018;7(Suppl 7):S779-S86. doi: 10.21037/tcr.2018.08.11.

5. Drilon A, Oxnard GR, Tan DSW, Loong HHF, Johnson M, Gainor J, et al. Efficacy of Selpercatinib in RET fusion-positive non-small-cell lung cancer. N Engl J Med. 2020;383(9):813-24. doi: 10.1056/NEJMoa2005653.

6. Cocco E, Scaltriti M, Drilon A: NTRK fusion-positive cancers and TRK inhibitor therapy. Nat Rev Clin Oncol 2018 Dec;15(12):731-747 doi: 10.1038/s41571-018-0113-0

7. Frampton GM, Ali SM, Rosenzweig M, Chmielecki J, Lu X, Bauer TM, 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;5(8):850-9. doi: 10.1158/2159-8290.CD-15-0285

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

Qualitative detection using the Idylla GeneFusion Assay is performed to detect rearrangements (fusions) within the ALK, ROS1 and RET genes, MET exon 14 skipping, and expression imbalance for ALK, ROS1, RET, NTRK1, NTRK2 and NTRK3 genes. See Targeted Genes and Methodology Details for MayoComplete Lung Rearrangements for details regarding the targeted gene regions evaluated by this test.(Unpublished Mayo method)

 

A pathology review and macro dissection to enrich for tumor cells are performed prior to slide scraping.

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.

4 to 8 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

FFPE tissue block: Unused portions of blocks will be returned within 10 to 14 days after testing is complete; FFPE tissue/cytology slides: Unused tissue slides are stored indefinitely; Digital images are obtained and stored for all slides used in testing

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.

81191

81193

81405

81479

81479 (if appropriate for government payers)

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
MCLNR MayoComplete Lung Rearrangements 73977-1
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.
618280 Result 82939-0
618281 Interpretation 69047-9
618282 Additional Info 48767-8
618283 Specimen 31208-2
618284 Tissue ID 80398-1
618285 Method 85069-3
618286 Disclaimer 62364-5
618287 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
Test Status - Test Delay 2022-10-24
New Test 2022-10-24