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Test Code ALKT ALK Mutation Analysis, Next-Generation Sequencing, Tumor


Ordering Guidance


Multiple oncology (cancer) gene panels are available. For more information see Hematology, Oncology, and Hereditary Test Selection 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.


Secondary ID

619694

Useful For

Identifying mutations within the ALK gene that predict resistance to ALK-inhibitors

Genetics Test Information

This test uses targeted next-generation sequencing to evaluate for somatic mutations within the ALK gene. See Targeted Genes and Methodology Details for ALK 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 ALK gene.

Highlights

This test evaluates formalin-fixed, paraffin-embedded tumor or cytology slides from patients with solid tumors for gene mutations in the ALK gene. Current data suggests that identifying an ALK gene mutation may predict resistance to ALK-inhibitors.

Disease States

  • Neuroblastoma

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.

Method Name

Sequence Capture Next-Generation Sequencing (NGS)

Reporting Name

ALK 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

Clinical Information

The ALK gene encodes anaplastic lymphoma kinase. Fusions of the ALK gene with a variety of 5’ (upstream) partner genes upregulate ALK’s kinase activity and contribute to tumorigenesis. ALK gene fusions have been reported in diverse tumor types. Numerous US Food and Drug Administration approved ALK-inhibitors have been developed for the treatment of tumors with ALK gene fusions. However, resistance to ALK inhibition can occur through the development of ALK gene mutations. This test can be used to identify ALK resistance mutations to aid in the management of these patients. In addition, ALK gain-of-function alterations have been reported in a subset of neuroblastomas.

Reference Values

An interpretive report will be provided.

Interpretation

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

Cautions

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 result does not rule out the presence of a variant that may be present but below the limits of detection of this assay. In a specimen with 20% or more tumor content, the analytical sensitivity of this assay for sequence reportable alterations is 5% mutant allele frequency with a minimum coverage of 500X.

 

Point mutations and small deletion-insertion mutations will be detected in the ALK gene only. This test may detect single exon deletions but does not detect multi-exon deletions, duplications, or genomic copy number variants.

 

Variant allele frequency (VAF) is the percentage of sequencing reads supporting a specific variant divided by the total sequencing reads at that position. In somatic testing, VAF should be interpreted in the context of several factors, including, but not limited to, tumor purity/heterogeneity/copy number status (ploidy, gains/losses, loss of heterozygosity) and sequencing artifact/misalignment.(1,2)

 

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, tumor sampling, histopathological, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion. 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.

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.

Clinical Reference

1. Strom SP. Current practices and guidelines for clinical next-generation sequencing oncology testing. Cancer Biol Med. 2016;13(1):3-11. doi:10.28092/j.issn.2095-3941.2016.0004

2. Spurr L, Li M, Alomran N, et al. Systematic pan-cancer analysis of somatic allele frequency. Sci Rep. 2018;8(1):7735. doi:10.1038/s41598-018-25462-0

3. Ou SI, Zhu VW, Nagasaka M: Catalog of 5' Fusion Partners in ALK-positive NSCLC Circa 2020. JTO Clin Res Rep. 2020 Feb 19;1(1):100015

4. Cooper AJ, Sequist LV, Lin JJ: Third-generation EGFR and ALK inhibitors: mechanisms of resistance and management. Nat Rev Clin Oncol. 2022 Aug;19(8):499-514

5. Schneider JL, Lin JJ, Shaw AT: ALK-positive lung cancer: a moving target. Nat Cancer. 2023 Mar;4(3):330-343

6. Trigg RM, Turner SD: ALK in Neuroblastoma: Biological and Therapeutic Implications. Cancers (Basel). 2018 Apr 10;10(4):113

7. Brady SW, Liu Y, Ma X, et al: Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations. Nat Commun. 2020 Oct 14;11(1):5183

Method Description

Next-generation sequencing is performed to evaluate the presence of a mutation in all coding regions of the ALK gene. See Targeted Genes and Methodology Details for ALK Mutation Analysis for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method)

 

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

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

Test Classification

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

CPT Code Information

88381-Microdissection, manual
81479

LOINC Code Information

Test ID Test Order Name Order LOINC Value
ALKT ALK Mutation Analysis, Tumor In Process

 

Result ID Test Result Name Result LOINC Value
619695 Result 82939-0
619696 Interpretation 69047-9
619697 Additional Information 48767-8
619698 Specimen 31208-2
619699 Tissue ID 80398-1
619700 Method 48767-8
619701 Disclaimer 62364-5
619702 Released By 18771-6

Forms

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