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HelpTest Code CMAPT Chromosomal Microarray, Tumor, Formalin-Fixed Paraffin-Embedded
Useful For
Genomic characterization of tumor for copy number imbalances and loss of heterozygosity
Assisting in the diagnosis and classification of malignant neoplasms
Evaluating the prognosis for patients with malignant tumors
Testing Algorithm
This test does not include a pathology consult. If a pathology consultation is requested, PATHC / Pathology Consultation should be ordered, and the appropriate fluorescence in situ hybridization (FISH) test will be ordered and performed at an additional charge.
Hematoxylin and eosin stain review of the paraffin-embedded sample is performed to identify the area of invasive tumor prior to DNA extraction and microarray analysis. If additional FISH testing is requested, it will be performed at an additional charge.
For more information see Aggressive B-cell Lymphoma Diagnostic Algorithm.
Method Name
Chromosomal Microarray (CMA)
Reporting Name
Chromosomal Microarray, Tumor, FFPESpecimen Type
VariesOrdering Guidance
This test is not performed on fresh tissue specimens. If testing is needed for fresh tissue specimens, order CMAT / Chromosomal Microarray, Tumor, Fresh or Frozen.
If a fresh tissue specimen is submitted, this test will be canceled and CMAT will be performed and charged.
Additional Testing Requirements
Necessary Information
A reason for testing and pathology report are required for testing to be performed. Send information with specimen. Acceptable pathology reports include working drafts, preliminary pathology or surgical pathology reports.
Specimen Required
Submit only 1 of the following specimens:
Specimen Type: Tissue
Container/Tube: Formalin-fixed, paraffin-embedded tumor tissue block
Specimen Type: Slides
Specimen Volume: 10 Consecutive, unstained, 5-micron-thick sections placed on positively charged slides and 1 hematoxylin and eosin-stained slide
Specimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Ambient (preferred) | ||
| Refrigerated | |||
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.Clinical Information
The importance of identifying chromosome abnormalities in malignant neoplasms is well established, and often provides important diagnostic, prognostic, and therapeutic information critical to proper patient management. Although many chromosomal abnormalities are large enough to be detected with conventional chromosome analysis, many others are below its limits of resolution, and conventional chromosome analysis does not detect copy-neutral loss of heterozygosity.
Chromosomal microarray (CMA) improves the diagnostic yield to identify genetic changes that are not detected by conventional chromosome analysis or fluorescence in situ hybridization (FISH) studies. CMA utilizes copy number probes and single nucleotide polymorphism probes to detect copy number changes and regions of copy-neutral loss of heterozygosity.
Chromosomal microarray analysis is appropriate to identify gain or loss of chromosome material throughout the genome at a resolution of 50 to 100 kilobases. CMA can:
-Define the size, precise breakpoints, and gene content of copy number changes to demonstrate the complexity of abnormalities
-Characterize unidentified chromosome material, marker chromosomes, and DNA amplification detected by conventional chromosome and FISH studies
-Determine if apparently balanced chromosome rearrangements identified by conventional chromosome studies have cryptic imbalances
-Assess regions of copy-neutral loss of heterozygosity, which is common in neoplasia and often masks homozygous mutations involving tumor suppressor genes
The limit of detection is dependent on size of the abnormality, type of abnormality (deletion or duplication) and DNA quality. When a deletion or duplication exceeds the reporting limits, mosaicism can confidently be detected as low as 25% and may be lower if the abnormality is large and DNA quality is good.
Reference Values
An interpretive report will be provided.
Interpretation
The interpretive report describes copy number changes and any loss of heterozygosity that may be associated with the neoplastic process. Abnormal clones with subclonal cytogenetic evolution will be discussed if identified.
The continual discovery of novel copy number variation and published clinical reports means that the interpretation of any given copy number change may evolve with increased scientific understanding.
Although the presence of a clonal abnormality usually indicates a neoplasia, in some situations it may reflect a benign or constitutional genetic change. If a genetic change is identified that is likely constitutional and clearly disease-associated (eg, XYY), follow-up with a medical genetic consultation may be suggested.
The absence of an abnormal clone may be the result of specimen collection from a site that is not involved in the neoplasm or may indicate that the disorder is caused by a point mutation that is not detectable by chromosomal microarray.
Chromosomal microarray, fluorescence in situ hybridization (FISH), and conventional cytogenetics are to some extent complementary methods. In some instances, additional FISH or conventional cytogenetic studies will be recommended to clarify interpretive uncertainties.
For more information and frequently asked questions, see Clarity on Reason for and Benefits of Chromosomal Microarray.
Cautions
This test is not approved by the US Food and Drug Administration, and it is best used as an adjunct to existing clinical and pathologic information.
This test does not detect balanced chromosome rearrangements such as reciprocal translocations, inversions, or balanced insertions.
This test does not detect point mutations, small deletions or insertions below the resolution of the assay, or other types of mutations such as epigenetic changes.
This test may not detect mosaic abnormalities in a minor proportion of cells, as such it is not recommended for minimal residual disease monitoring or for specimens with tumor proportions less than approximately 20% of sample.
The results of this test may reveal incidental findings unrelated to the original reason for referral.
Supportive Data
The chromosomal microarray was validated on the Affymetrix OncoScan platform in a study of 50 specimens from a variety of tumors including glioma, breast, and melanoma. Results were correlated with the pathology report, fluorescence in situ hybridization, or other results.
Clinical Reference
1. Mikhail FM, Biegel JA, Cooley LD, et al. Technical laboratory standards for interpretation and reporting of acquired copy-number abnormalities and copy-neutral loss of heterozygosity in neoplastic disorders: a joint consensus recommendation from the American College of Medical Genetics and Genomics (ACMG) and the Cancer Genomics Consortium (CGC). Genet Med. 2019;21(9):1903-1916
2. Chun K, Wenger GD, Chaubey A, et al. Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia. Cancer Genet. 2018;228-229:236-250
3. Shao L, Akkari Y, Cooley LD, et al. Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2021;23(10):1818-1829
4. Wang Y, Cottman M, Schiffman JD. Molecular inversion probes: a novel microarray technology and its application in cancer research. Cancer Genet. 2012;205(7-8):341-355
Method Description
The selection of tissue and the identification of invasive tumor on the hematoxylin and eosin (H and E)-stained slide are performed by a pathologist. Using the H and E slide as a reference, the target areas are marked on the unstained slide, the DNA is extracted from the tumor is labeled and hybridized to the microarray. Following hybridization, the microarray is scanned, and the intensity of signals is measured and compared to a reference data set. These data are used to determine copy number changes and regions with loss of heterozygosity. Chromosomal microarray data alone does not provide information about the structural nature of an imbalance. Thus, it may be of benefit to utilize fluorescence in situ hybridization or additional techniques to further characterize a patient sample.(Unpublished Mayo method)
Day(s) Performed
Monday through Friday
Report Available
10 to 21 daysSpecimen Retention Time
Slides and hematoxylin and eosin used for analysis are retained by the lab indefinitely. Client provided paraffin blocks and extra unstained slides (if provided) will be returned after testing is complete.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
81277
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| CMAPT | Chromosomal Microarray, Tumor, FFPE | 94087-4 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 54735 | Result Summary | 50397-9 |
| 54736 | Result | 62356-1 |
| 54737 | Nomenclature | 62378-5 |
| 54738 | Interpretation | 69965-2 |
| CG908 | Reason for Referral | 42349-1 |
| 54744 | Specimen | 31208-2 |
| 54739 | Source | 31208-2 |
| 54740 | Tissue ID | 80398-1 |
| 54741 | Method | 85069-3 |
| 53425 | Additional Information | 48767-8 |
| 54742 | Released By | 18771-6 |
Special Instructions
Forms
If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.