Test Id : CMAT
Chromosomal Microarray, Tumor, Fresh or Frozen
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, including hematolymphoid malignancies
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.
DNA is extracted from the specimen prior to hybridization to the microarray.
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
CytoScan
Oncology Array
Oncologic Array
Onc Array
Loss of Heterozygosity (LOH)
Copy Number Loss of Heterozygosity (cnLOH)
Fresh Tumor Array
Accel
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
DNA is extracted from the specimen prior to hybridization to the microarray.
Specimen Type
Describes the specimen type validated for testing
Varies
Ordering Guidance
This test is not performed on formalin-fixed, paraffin-embedded (FFPE) specimens. If testing is needed for FFPE specimens, order CMAPT / Chromosomal Microarray, Tumor, Formalin-Fixed Paraffin-Embedded.
If an FFPE specimen is submitted, this test will be canceled and CMAPT / Chromosomal Microarray, Tumor, Formalin-Fixed Paraffin-Embedded will be added and performed as the appropriate test.
Shipping Instructions
Advise Express Mail or equivalent if not on courier service.
Necessary Information
1. A reason for testing must be provided for testing to be performed.
2. A pathology report should accompany the specimen. If this information is not available at the time of order, submit as soon as possible for appropriateness of testing and to aid in interpretation of results.
ORDER QUESTIONS AND ANSWERS
| Question ID | Description | Answers |
|---|---|---|
| CG905 | 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:
Supplies: Hank's Solution (T132)
Specimen Type: Tumor biopsy
Container/Tube: Sterile container with sterile Hank's balanced salt solution, Ringer's solution, or normal saline
Specimen Volume: 0.5-3 cm(3) or larger
Specimen Type: Lymph node
Container/Tube: Sterile container with sterile Hank's balanced salt solution, Ringer's solution, or normal saline.
Specimen Volume: 1 cm(3)
Specimen Type: Skin biopsy
Container/Tube: Sterile container with sterile Hank's balanced salt solution, Ringer's solution, or normal saline.
Specimen Volume: 4-mm diameter
Collection Instructions:
1. Wash biopsy site with an antiseptic soap.
2. Thoroughly rinse area with sterile water.
3. Do not use alcohol or iodine preparations.
4. A local anesthetic may be used.
5. Biopsy specimens are best taken by punch biopsy to include full thickness of dermis.
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.
Tumor biopsy: 3 cm(3); Lymph node: 1 cm(3); Skin biopsy: 4 mm diameter
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, including hematolymphoid malignancies
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.
DNA is extracted from the specimen prior to hybridization to the microarray.
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 greater than 2 million copy number probes and approximately 750,000 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 30 to 60 kilobases.
CMA can:
-Define the size, 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 loss of heterozygosity that may be associated with the neoplastic process being evaluated. Abnormal clones with subclonal abnormalities will be discussed if identified.
The continual discovery and publication of novel copy number abnormalities and losses of heterozygosity associated with neoplastic processes means that the interpretation of any given detected abnormality may change with increased scientific understanding.
Although the presence of a clonal abnormality is usually associated with 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 pathogenic or likely pathogenic and/or related to the clinical reason for referral, this will be included in the report and 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.
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/pathogenic variants, small insertions or deletions, trinucleotide repeat expansions, or other copy number abnormalities below the resolution of the assay, or other types of variants such as epigenetic changes.
This test may not detect mosaic abnormalities in small proportion of cells, and as such it is not recommended for minimal residual disease monitoring or for specimens with tumor contents less than 20% of sample.
The results of this test may reveal incidental and secondary findings unrelated to the original reason for referral.
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. doi:10.1038/s41436-019-0545-7
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. doi:10.1016/j.cancergen.2018.07.004
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. doi:10.1038/s41436-021-01214-
Method Description
Describes how the test is performed and provides a method-specific reference
DNA 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 Sunday
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 |
|---|---|---|
| CMAT | Chromosomal Microarray, Tumor | 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.
|
|---|---|---|
| 54728 | Result Summary | 50397-9 |
| 54729 | Result | 62356-1 |
| 54730 | Nomenclature | 62356-1 |
| 54731 | Interpretation | 69965-2 |
| CG905 | Reason for Referral | 42349-1 |
| 54743 | Specimen | 31208-2 |
| 54732 | Source | 31208-2 |
| 54733 | Method | 85069-3 |
| 53424 | Additional Information | 48767-8 |
| 54734 | Released By | 18771-6 |