Test Catalog

Test ID: CMACB    
Chromosomal Microarray, Congenital, Blood

Useful For Suggests clinical disorders or settings where the test may be helpful

First-tier, postnatal testing for individuals with multiple anomalies that are not specific to well-delineated genetic syndromes, apparently nonsyndromic developmental delay or intellectual disability, or autism spectrum disorders as recommended by the American College of Medical Genetics and Genomics (ACMG)


Follow-up testing for individuals with unexplained developmental delay or intellectual disability, autism spectrum disorders, or congenital anomalies with a previously normal conventional chromosome study


Determining the size, precise breakpoints, gene content, and any unappreciated complexity of abnormalities detected by other methods such as conventional chromosome and fluorescence in situ hybridization (FISH) studies


Determining if apparently balanced abnormalities identified by previous conventional chromosome studies have cryptic imbalances, since a proportion of such rearrangements that appear balanced at the resolution of a chromosome study are actually unbalanced when analyzed by higher-resolution chromosomal microarray


Assessing regions of homozygosity related to uniparental disomy or identity by descent

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

This test is not appropriate for detecting acquired copy number changes and excessive homozygosity. If this test is ordered with a reason for referral indicating a hematological disorder, the test will be cancelled and CMAH / Chromosomal Microarray, Hematologic Disorders, Varies will be performed as the appropriate test.


The following algorithms are available in Special Instructions:

-Epilepsy: Unexplained Refractory and/or Familial Testing Algorithm

-Prader-Willi and Angelman Syndromes: Laboratory Approach to Diagnosis

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Aneuploidy or unbalanced chromosome rearrangements are often found in patients with intellectual disability, developmental delay, autism, dysmorphic features, or congenital anomalies. Some chromosomal abnormalities are large enough to be detected with conventional chromosome analysis. However, many pathogenic rearrangements are below the resolution limits of chromosome analysis (approximately 5 megabases). Chromosomal microarray (CMA) is a high-resolution method for detecting copy number changes (gains or losses) across the entire genome in a single assay and is sometimes called a molecular karyotype.


This CMA test utilizes greater than 1.9 million copy number probes and approximately 750,000 single nucleotide polymorphism probes for the detection of copy number changes and regions of excessive homozygosity. Identification of regions of excessive homozygosity on a single chromosome could suggest uniparental disomy (UPD), which may warrant further clinical investigation when observed on chromosomes with known imprinting disorders associated with UPD. In addition, the detection of excessive homozygosity on multiple chromosomes may suggest consanguinity and, therefore, could be useful in determining candidate genes for further testing for autosomal recessive disorders.


An online research opportunity called GenomeConnect (genomeconnect.org) is available for the recipients of genetic test results. This patient registry collects deidentified genetic and health information to advance knowledge of genetic variants. See GenomeConnect Patient Portal in Special Instructions for more information.

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

When interpreting results, the following factors need to be considered:

Copy number variation is found in all individuals, including patients with abnormal phenotypes and normal populations. Therefore, determining the clinical significance of a rare or novel copy number change can be challenging. Parental testing may be necessary to further assess the potential pathogenicity of a copy number change.


While most copy number changes observed by chromosomal microarray testing can readily be characterized as pathogenic or benign, there are limited data available to support definitive classification of a subset into either of these categories. In these situations, a number of considerations are taken into account to help interpret results including the size and gene content of the imbalance, whether the change is a deletion or duplication, the inheritance pattern, and the clinical and/or developmental history of a transmitting parent.


All copy number variants within the limit of detection classified as pathogenic or likely pathogenic will be reported regardless of size. This includes but is not limited to incidental findings currently recommended for reporting by the American College of Medical Genetics and Genomics (ACMG).(1) Copy number changes with unknown significance will be reported when at least one protein-coding gene is involved in a deletion greater than 200 kilobases (kb) or a duplication greater than 1 megabase (Mb).


The detection of excessive homozygosity may suggest the need for additional clinical testing to confirm uniparental disomy (UPD) or to test for variants in genes associated with autosomal recessive disorders consistent with the patient's clinical presentation that are present in regions of homozygosity. Interstitial regions with absence of heterozygosity (AOH) of unknown significance will be reported when greater than 10 Mb on UPD-associated chromosomes, and greater than 15 Mb on non-imprinted chromosomes. Terminal AOH will be reported when greater than 5 Mb. Whole genome AOH will be reported when greater than 2% of the genome.


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.


Families benefit from hearing genetic information multiple times and in multiple ways. A referral to a clinical genetics professional is appropriate for individuals and families to discuss the results of chromosomal microarray testing.

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.


Chromosomal microarray data alone does not provide information about the structural nature of an imbalance.


This test does not detect balanced chromosome rearrangements such as Robertsonian or other reciprocal translocations, inversions, or balanced insertions.


This test does not detect all types and instances of uniparental disomy.


This test is not designed to detect mosaicism, although it can be detected in some cases.


This test does not detect point alterations, small deletions or insertions below the resolution of this assay, or other types of variants such as epigenetic changes.


The results of this test may reveal incidental findings not related to the original reason for referral. In such cases, studies of additional family members may be required to help interpret the results.


Families benefit from hearing genetic information multiple times and in multiple ways. A referral to a clinical genetics professional is appropriate for individuals and families to discuss the results of chromosomal microarray testing.


Interfering factors:

-Use of an improper anticoagulant (sodium heparin is best) or improperly mixing the blood with the anticoagulant

-Excessive transport time

-Inadequate amount of blood

-Improper packaging may result in broken, leaky, and contaminated specimen during transport

Supportive Data

The array was validated by testing 113 specimens previously tested using another array platform, chromosome analysis, fluorescence in situ hybridization (FISH) analysis, or a polymerase chain reaction (PCR)-based assay. The study set included specimens from phenotypically normal individuals, and patients identified with a gain or loss of an autosome or sex chromosome or identified with uniparental disomy. All abnormalities were confirmed.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Kalia, S., Adelman, K., Bale, S. et al: Recommendations for reporting of secondary findings in clinical exome and genome sequencing. 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genet Med. 2017;19:249-255

2. Manning M, Hudgins L: Professional Practice and Guidelines Committee: Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med. 2010;12(11):742-745

3. Miller DT, Adam MP, Aradhya S, et al: Consensus statement: Chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86:749-764

4. Kearney HM, Thorland EC, Brown KK, et al: American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 2011;13(7)680-685

5. Kearney HM, Kearney JB, Conlin LK: Diagnostic implications of excessive homozygosity detected by SNP-based microarrays: consanguinity, uniparental disomy, and recessive single-gene mutations. Clin Lab Med. 2011;31(4):595-613

6. Marcou CA, Pitel B, Hagen CE, et al: Limited diagnostic impact of duplications <1?Mb of uncertain clinical significance: a 10-year retrospective analysis of reporting practices at the Mayo Clinic [published online ahead of print, 2020 Aug 21]. Genet Med. 2020. doi: 10.1038/s41436-020-0932-0

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