Test Catalog

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.

 

If a fresh tissue specimen is submitted, this test will be cancelled and CMAT / Chromosomal Microarray, Tumor will be performed.

 

See Aggressive B-cell Lymphoma Diagnostic Algorithm in Special Instructions.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

Chromosomal Microarray (CMA) using Applied Biosystems (Affymetrix) Oncoscan

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Chromosomal Microarray, Tumor, FFPE

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.

 

If a fresh tissue specimen is submitted, this test will be cancelled and CMAT / Chromosomal Microarray, Tumor will be performed.

 

See Aggressive B-cell Lymphoma Diagnostic Algorithm in Special Instructions.

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 using Affymetrix Cytoscan HD.

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

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

See Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

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.

 

If a fresh tissue specimen is submitted, this test will be cancelled and CMAT / Chromosomal Microarray, Tumor will be performed.

 

See Aggressive B-cell Lymphoma Diagnostic Algorithm in Special Instructions.

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.

 

CMA 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 pathogenic (eg, XYY), follow-up with a medical genetics 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 (CMA).

 

CMA, 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.

 

See Cytogenetic Analysis of Glioma in Special Instructions for common questions and answers.

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 FDA 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. Cooley L, Lebo M, Li M, et al: American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. Genet Med. 2013;15:484-494. doi: 10.1038/gim.2013.49

2. Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C: Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013 Sep 26;45(10):1127-1133. doi: 10.1038/ng.2762

3. Wang Y, Cottman M, Schiffman JD: Molecular inversion probes: a novel microarray technology and its application in cancer research. Cancer Genet. 2012 Jul-Aug;205(7-8):341-355. doi: 10.1016/j.cancergen.2012.06.005

Special Instructions
Library of PDFs including pertinent information and forms related to the test

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

No

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.

10 to 21 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Slides and H and E 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 Location
Indicates the location of the laboratory that performs the test

Rochester

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 Regional Manager. 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. This test 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.

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

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports

Test Update Resources

Change Type Effective Date
Test Status - Test Resumed 2021-05-06