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Test Code NTRKM NTRK Genes Mutation Analysis, Next-Generation Sequencing, Tumor


Ordering Guidance


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



Necessary Information


A 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


This assay requires at least 20% tumor nuclei.

-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue 216 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 4 mm x 4 mm x 10 slides as preferred: approximate/equivalent to 144 mm(2) and the minimum as 3 mm x 1 mm x 10 slides: approximate/equivalent to 36 mm(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.

Additional Information: Unused unstained slides will not be returned.

 

Specimen Type: Cytology slide (direct smears or ThinPrep)

Slides: 1 to 3 Slides

Collection Instructions: Submit 1 to 3 slides stained and coverslipped 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.


Useful For

Identifying NTRK mutations that may predict resistance to Trk inhibitors

Genetics Test Information

This test uses targeted next-generation sequencing to evaluate for somatic mutations within the NTRK1, NTRK2, and NTRK3 genes. See Targeted Genes and Methodology Details for NTRK Genes Mutation Analysis for details regarding the targeted gene regions evaluated by this test.

 

This test is performed to evaluate for somatic mutations within solid tumor samples. This test does not assess for germline alterations within the genes listed.

Additional Tests

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

Testing Algorithm

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

Reporting Name

NTRK Genes Mutation Analysis, Tumor

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

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

Reject Due To

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

Reference Values

An interpretive report will be provided.

Supportive Data

Performance Characteristics:

The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and deletions-insertions [delins, formerly indel]) is 5% variant allele frequency (VAF) and having at least 500x deduplicated coverage.

 

Verification studies demonstrated concordance between this test and the reference method for detection of SNV and delins is 98.5% (673/683) and 98.4% (122/124) of variants, respectively. Concordance for the detection of delins was 99.0% (100/101) in variants 1 to 10 base pairs (bp) in size, 93.3% (14/15) in variants 11 to 50 bp in size, and 100% (8/8) in variants over 50 bp in size.

 

To ensure accuracy, this test will be performed on cases that are estimated by a pathologist to have at least 20% tumor cells.

Day(s) Performed

Monday through Friday

Report Available

12 to 20 days

Specimen Retention Time

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

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

88381-Microdissection, manual

81479

LOINC Code Information

Test ID Test Order Name Order LOINC Value
NTRKM NTRK Genes Mutation Analysis, Tumor 105596-1

 

Result ID Test Result Name Result LOINC Value
619704 Result 82939-0
619705 Interpretation 69047-9
619706 Additional Information 48767-8
619707 Specimen 31208-2
619708 Tissue ID 80398-1
619709 Method 85069-3
619710 Disclaimer 62364-5
619711 Released By 18771-6

Forms

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