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Test ID: CMAT Chromosomal Microarray, Tumor, Fresh or Frozen using Affymetrix Cytoscan HD

Useful For

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

DNA is extracted from the specimen prior to hybridization to the microarray. An unstimulated cell culture will be set up on all specimens with adequate volume and held pending additional testing. If additional testing is requested, such as karyotype analysis or FISH, it will be performed at an additional charge.

Method Name

Chromosomal Microarray (CMA) using Affymetrix Cytoscan HD

Reporting Name

Chromosomal Microarray, Tumor

Specimen Type


Advisory Information


Additional Testing Requirements

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

Necessary Information

Provide a reason for referral with each specimen. The laboratory will not reject testing if this information is not provided, but appropriate testing and interpretation may be compromised or delayed. Include pathology reports, if available.

Specimen Required

Submit only 1 of the following specimens:


Specimen Type: Tumor biopsy

Supplies: Hank's Solution (T132)

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline

Specimen Volume: 0.5-3 cm(3) or larger


Specimen Type: Lymph node

Supplies: Hank's Solution (T132)

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline.

Specimen Volume: 1 cm(3)


Specimen Type: Skin biopsy

Supplies: Hank's Solution (T132)

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), 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

Tumor Biopsy: 3 cm(3)
Lymph Node: 1 cm(3)
Skin Biopsy: 4 mm diameter

Specimen Stability Information

Specimen Type Temperature Time
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 greater than 1.9 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.  


CMA 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, 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.

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

Day(s) and Time(s) Performed

Samples processed Monday through Sunday. Results reported Monday through Friday, 8 a.m.-5 p.m., CST

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
CMAT Chromosomal Microarray, Tumor In Process


Result ID Test Result Name Result LOINC Value
54729 Result 62356-1
54730 Nomenclature 62356-1
54728 Result Summary 50397-9
54731 Interpretation 69965-2
CG905 Reason for Referral 42349-1
54743 Specimen 31208-2
54732 Source 31208-2
54733 Method 49549-9
53424 Additional Information 48767-8
54734 Released By 18771-6


If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.

Mayo Clinic Laboratories | Oncology Catalog Additional Information:

MML-Bone-and-Soft-Tissue-Cancer, MML-Breast-Cancer, MML-Endocrine-Cancer, MML-Gastrointestinal-Cancer, MML-Gynegological-Cancer, MML-Head-Neck-Cancer, MML-Neuro-Oncology-oms, MML-Pulmonary-Cancer, MML-Skin-Cancer, mml-Genitourinary-Cancer