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Test ID: 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 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 specimen or specimen in fixative is submitted, ANPAT / Anatomic Pathology Consultation, Wet Tissue will be added by the laboratory, at an additional charge, to facilitate the performance of this test.   


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

Method Name

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

Reporting Name

Chromosomal Microarray, Tumor, FFPE

Specimen Type


Advisory Information


Additional Testing Requirements

If a fresh specimen or specimen in fixative is submitted, ANPAT / Anatomic Pathology Consultation, Wet Tissue will be added by the laboratory, at an additional charge, to facilitate the performance of this test.

Necessary Information

A reason for referral and pathology report are required in order 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)

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 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

An interpretive report will be provided.


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, 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.

Clinical Reference

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

2. Ciriello G, Miller ML, Aksoy BA, et al: Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013 Sep 26;45(10):1127-1133

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

Day(s) and Time(s) Performed

Specimens are processed Monday through Sunday.

Results reported Monday through Friday, 8 a.m.-5 p.m.

Analytic Time

10 days

Test Classification

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 U.S. Food and Drug Administration.

CPT Code Information


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 49549-9
53425 Additional Information 48767-8
54742 Released By 18771-6
Mayo Clinic Laboratories | Hematology Catalog Additional Information: