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
This test is not intended for use for hematological malignancies.
This test uses next-generation sequencing to identify rearrangements (fusions) involving ALK, ROS1, RET, and NTRK1. See 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 rearrangements (fusions) within solid tumor samples.
This test evaluates formalin-fixed, paraffin-embedded tumor or cytology slides from patients with lung cancer for rearrangements (fusions) to identify candidates for targeted therapy.
Current data suggests that lung carcinomas with ALK rearrangements may be sensitive to ALK inhibitors.
Test Id | Reporting Name | Available Separately | Always Performed |
---|---|---|---|
SLIRV | Slide Review in MG | No, (Bill Only) | Yes |
When this test is ordered, slide review will always be performed at an additional charge.
Polymerase Chain Reaction (PCR)-Based Next Generation Sequencing
ALK
ROS1
RET
NTRK1
Lung cancer rearrangement
Lung cancer fusion
Next Gen Sequencing Test
NGS
When this test is ordered, slide review will always be performed at an additional charge.
Varies
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
This assay requires at least 20% tumor nuclei.
-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue180 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.
If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.
See Specimen Required
Other | Specimens that have been decalcified (all methods) Specimens that have not been formalin-fixed, paraffin-embedded |
Specimen Type | Temperature | Time | Special Container |
---|---|---|---|
Varies | Ambient (preferred) | ||
Frozen | |||
Refrigerated |
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
This test is not intended for use for hematological malignancies.
This test uses next-generation sequencing to identify rearrangements (fusions) involving ALK, ROS1, RET, and NTRK1. See 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 rearrangements (fusions) within solid tumor samples.
When this test is ordered, slide review will always be performed at an additional charge.
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 test uses formalin-fixed paraffin-embedded tissue or cytology slides to assess for common rearrangements (fusions) involving 4 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 Activated/Partner Gene Breakpoints Resulting in Targeted Fusion Transcripts Interrogated by Lung Panel for details regarding the targeted gene regions evaluated by this test.
An interpretative report will be provided.
An interpretive report will be provided.
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 (wild-type) 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) involving ALK, ROS1, RET and NTRK1 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 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.
We have developed a next-generation sequencing assay to detect 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.
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.
1. Mok TS: Personalized medicine in lung cancer: What we need to know. Nat Rev Clin Oncol 2011;8:661-668
2. Cheng L, Alexander RE, Maclennan GT, et al: Molecular pathology of lung cancer: key to personalized medicine. Mod Path 2012;25(3):346-369
3. Takeuchi K, Soda M, Togashi Y, et al: RET, ROS1 and ALK fusions in lung cancer. Nat Med 2012;18(3):378-381
4. 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
Next-generation sequencing is performed to test for the presence of rearrangements involving the ALK, ROS1, RET, and NTRK1 genes. See Activated/Partner Gene Breakpoints Resulting in Targeted Fusion Transcripts Interrogated by Lung Panel for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method)
Monday through Friday
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.
81405-RET
81479-(ROS1, ALK, NTKR1)
Slide Review
88381-Microdissection, manual
Test Id | Test Order Name | Order LOINC Value |
---|---|---|
LUNGR | Lung Rearrangement Testing, 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.
|
---|---|---|
43702 | Result Summary | 50397-9 |
43703 | Result | 95123-6 |
44138 | Interpretation | 69047-9 |
44139 | Additional Information | 48767-8 |
44140 | Specimen | 31208-2 |
44141 | Source | 31208-2 |
46911 | Tissue ID | 80398-1 |
44142 | Released By | 18771-6 |