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HelpTest Code MYODT MYOD1 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
619685Useful For
Identifying specific mutations within the MYOD1 gene to assist in tumor diagnosis/classification
Assisting in the clinical management of patients with spindle cell and sclerosing rhabdomyosarcoma
Highlights
This test evaluates formalin-fixed, paraffin-embedded tumor or cytology slides from patients with solid tumors for specific gene mutations in the MYOD1 gene. Identifying a MYOD1 gene mutation may be of diagnostic and clinical management significance for spindle cell/sclerosing rhabdomyosarcoma.
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.
Special Instructions
Method Name
Sequence Capture Next-Generation Sequencing (NGS)
Reporting Name
MYOD1 Mutation Analysis, TumorSpecimen Type
VariesSpecimen 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 MYOD1 gene, an oncogene, encodes Myoblast determination protein 1, MyoD1, a transcription factor involved in the control of muscle cell differentiation. MYOD1-mutant spindle cell/sclerosing rhabdomyosarcoma is a distinct entity in the 2020 World Health Organization classification of soft tissue and bone tumors.(1) MYOD1 L122R is a missense alteration located in the basic helix–loop–helix DNA-binding domain of the MyoD1 protein and is a recurrent alteration in spindle cell/sclerosing rhabdomyosarcoma. MYOD1 L122R mutation has been associated with poor prognosis in rhabdomyosarcoma.
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 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 MYOD1 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.(2,3)
Rare alterations (ie, polymorphisms) may be present that could lead to false-negative or false-positive results.
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 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 pair (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. Anderson WJ, Doyle LA: Updates from the 2020 World Health Organization Classification of soft tissue and bone tumours. Histopathology. 2021 Apr;78(5):644-657
2. 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
3. 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
4. Berkes CA, Tapscott SJ: MyoD and the transcriptional control of myogenesis. Semin Cell Dev Biol. 2005 Aug-Oct;16(4-5):585-595
5. Kohsaka S, Shukla N, Ameur N: A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations. Nat Genet. 2014 Jun;46(6):595-600
6. Rekhi B, Upadhyay P, Ramteke MP, Dutt A: MYOD1 (L122R) mutations are associated with spindle cell and sclerosing rhabdomyosarcomas with aggressive clinical outcomes. Mod Pathol. 2016 Dec;29(12):1532-1540
7. Agaram NP, LaQuaglia MP, Alaggio R: MYOD1-mutant spindle cell and sclerosing rhabdomyosarcoma: an aggressive subtype irrespective of age. A reappraisal for molecular classification and risk stratification. Mod Pathol. 2019 Jan;32(1):27-36
8. Shern JF, Selfe J, Izquierdo E: Genomic classification and clinical outcome in rhabdomyosarcoma: a report from an international consortium. J Clin Oncol. 2021 Sep 10;39(26):2859-2871
Method Description
Next-generation sequencing is performed to evaluate the presence of a mutation in all coding regions of the MYOD1 gene. See Targeted Gene Regions Interrogated for MYOD1 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 daysSpecimen 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 |
|---|---|---|
| MYODT | MYOD1 Mutation Analysis, Tumor | 105595-3 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 619686 | Result | 82939-0 |
| 619687 | Interpretation | 69047-9 |
| 619688 | Additional Information | 48767-8 |
| 619689 | Specimen | 31208-2 |
| 619690 | Tissue ID | 80398-1 |
| 619691 | Method | 48767-8 |
| 619692 | Disclaimer | 62364-5 |
| 619693 | Released By | 18771-6 |
Forms
If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.