Test Catalog

Test Id : CMACB

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Chromosomal Microarray, Congenital, Blood

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Overview

Test Catalog

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

 

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 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.

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

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, Blood

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

CytoScan

Congenital Array

Constitutional Array

Absence of Heterozygosity (AOH)

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

Specimen Type
Describes the specimen type validated for testing

Whole blood

Ordering Guidance

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

Necessary Information

The reason for testing is required.

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
CG779 Reason for Referral

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

This test requires 2 blood specimens: 1 sodium heparin and 1 EDTA. Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube: Green top (sodium heparin) and lavender top (EDTA)

Specimen Volume: 3-mL EDTA tube and 4-mL sodium heparin tube

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole blood specimens in original tubes. Do not aliquot.

 

Specimen Type: Cord blood

Container/Tube: Green top (sodium heparin) and lavender top (EDTA)

Specimen Volume: 3-mL EDTA tube and 4-mL sodium heparin tube

Note: The lab will attempt testing on a minimum of 1-mL whole blood, EDTA preferred.

Collection Instructions:

1. Invert several times to mix blood.

2. Send cord blood specimens in original tubes. Do not aliquot.

3. Label specimen as cord blood.

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

Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Chromosomal Microarray Patient Information (T665)

3. Family Member Phenotype Information for Genomic Testing

4. If not ordering electronically, complete, print, and send a Neurology Specialty Testing Client Test Request (T732) with the specimen.

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

2 mL

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
Whole blood Ambient (preferred)
Refrigerated

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

 

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 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.

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. For more information see GenomeConnect Patient Portal.

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 SS, Adelman K, Bale SJ, 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 Feb;19(2):249-255. doi: 10.1038/gim.2016.190

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 Nov;12(11):742-745. doi: 10.1097/GIM.0b013e3181f8baad

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 May;86(5):749-764. doi: 10.1016/j.ajhg.2010.04.006

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 Jul;13(7)680-685. doi: 10.1097/GIM.0b013e3182217a3a

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 Dec;31(4):595-613. doi: 10.1016/j.cll.2011.08.003

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. Genet Med. 2020 Dec;22(12):2120-2124. doi: 10.1038/s41436-020-0932-0

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

DNA extracted from the patient's peripheral blood 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 of excess homozygosity. Chromosomal microarray data alone does not provide information about the structural nature of an imbalance and some abnormal results may be characterized by fluorescence in situ hybridization (FISH), limited chromosome analysis, or additional techniques.(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.

8 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

Four weeks

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.

81229

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
CMACB Chromosomal Microarray, Blood 62343-9
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.
52399 Result Summary 50397-9
52400 Result 82939-0
54643 Nomenclature 62378-5
52401 Interpretation 69965-2
CG779 Reason For Referral 42349-1
54713 Specimen 31208-2
52402 Source 31208-2
52403 Method 85069-3
52404 Released By 18771-6
55128 Additional Information 48767-8

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