Test Id : CMAPT
Chromosomal Microarray, Tumor, Formalin-Fixed Paraffin-Embedded
Useful For
Suggests clinical disorders or settings where the test may be helpful
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
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
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
A short description of the method used to perform the test
Chromosomal Microarray (CMA)
NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.
Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test
Aliases
Lists additional common names for a test, as an aid in searching
aCGH
Array CGH
Array Comparative Genomic Hybridization
Oligonucleotide Array
Oligo Array
Single Nucleotide Polymorphism (SNP) Array
Whole Genome Array
Microarray
Molecular Karyotype
OncoScan
Oncology Array
Oncologic Array
Onc Array
Loss of Heterozygosity (LOH)
Copy Neutral Loss of Heterozygosity (cnLOH)
BRAF KIAA1549 Fusion
1p 19q Co-Deletion
Paraffin Embedded Tumor Array
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
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.
Specimen Type
Describes the specimen type validated for testing
Varies
Ordering 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.
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.
ORDER QUESTIONS AND ANSWERS
| Question ID | Description | Answers |
|---|---|---|
| CG908 | Reason for Referral |
Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing
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
Special Instructions
Library of PDFs including pertinent information and forms related to the test
Forms
If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.
Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the testing laboratory. The minimum volume is sufficient for one attempt at testing.
See Specimen Required
Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected
Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Ambient (preferred) | ||
| Refrigerated | |||
Useful For
Suggests clinical disorders or settings where the test may be helpful
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
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
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.
Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test
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
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.
An interpretive report will be provided.
Interpretation
Provides information to assist in interpretation of the test results
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
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances
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
Recommendations for in-depth reading of a clinical nature
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
Describes how the test is performed and provides a method-specific reference
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)
PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information
Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.
Monday through Friday
Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.
Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location
Indicates the location of the laboratory that performs the test
Fees :
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.
- Authorized users can sign in to Test Prices for detailed fee information.
- Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
- Prospective clients should contact their account representative. For assistance, contact Customer Service.
Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.
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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.
CPT codes are provided by the performing laboratory.
CPT codes are provided by the performing laboratory.
81277
LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.
| Test Id | Test Order Name | Order LOINC Value |
|---|---|---|
| CMAPT | Chromosomal Microarray, Tumor, FFPE | 94087-4 |
| 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.
|
|---|---|---|
| 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 |