Test Catalog

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

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. 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.

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 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 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, 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, 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 CytoScan HD platform in a study of 58 specimens from a variety of tumors including liver, breast, kidney, lung, and brain. Results were correlated to previous conventional karyotype and FISH analysis, when available.

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

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