Test Catalog

Test Id : CMAP

Chromosomal Microarray, Prenatal, Amniotic Fluid/Chorionic Villus Sampling

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

Prenatal diagnosis of copy number changes (gains or losses) across the entire genome

 

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

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

Cultures from this specimen will be discarded 10 days after all cytogenetic test results have been reported. If further testing is desired, call the laboratory at 800-533-1710.

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

Maternal cell contamination (MCC) testing will be performed at no additional charge if a maternal blood sample is received to rule out the presence of maternal cells in the prenatal sample, see Additional Testing Requirements.

 

If an insufficient sample is received or MCC is identified in the prenatal sample, microarray testing will be performed on cultured material.

 

For more information see Prenatal Aneuploidy Screening and Diagnostic Testing Options

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, Prenatal

Aliases
Lists additional common names for a test, as an aid in searching

Oligonucleotide Array

Oligo Array

Single Nucleotide Polymorphism (SNP) Array

Whole Genome Array

Molecular Karyotype

Constitutional Array

Prenatal Diagnosis

aCGH or array CGH (Array Comparative Genomic Hybridization)

Amniotic fluid

Chorionic villi sample or CVS

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

Maternal cell contamination (MCC) testing will be performed at no additional charge if a maternal blood sample is received to rule out the presence of maternal cells in the prenatal sample, see Additional Testing Requirements.

 

If an insufficient sample is received or MCC is identified in the prenatal sample, microarray testing will be performed on cultured material.

 

For more information see Prenatal Aneuploidy Screening and Diagnostic Testing Options

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

This test does not detect balanced chromosome rearrangements such as Robertsonian or other reciprocal translocations, inversions, or balanced insertions. These abnormalities may be identified by chromosome analysis (see CHRAF / Chromosome Analysis, Amniotic Fluid or CHRCV / Chromosome Analysis, Chorionic Villus Sampling).

 

If the reason for testing or specimen type received indicates a fetal demise, the test will be cancelled and CMAPC / Chromosomal Microarray, Autopsy, Products of Conception, or Stillbirth will be added and performed as the appropriate test.

Additional Testing Requirements

A maternal blood sample is requested when ordering this test (see PPAP / Parental Sample Prep for Prenatal Microarray Testing); the PPAP test must be ordered under a different order number than the prenatal specimen.

 

A paternal blood sample is desired but not required (see PPAP / Parental Sample Prep for Prenatal Microarray Testing).

 

Portions of the specimen may be used for other tests such as measuring markers for neural tube defects (eg, AFPA / Alpha-Fetoprotein, Amniotic Fluid), molecular genetic testing, biochemical testing, and chromosome and FISH testing (including CHRAF / Chromosome Analysis, Amniotic Fluid; CHRCV / Chromosome Analysis, Chorionic Villus Sampling; and PADF / Prenatal Aneuploidy Detection, FISH).

 

If additional molecular genetic or biochemical genetic testing is needed, order CULAF / Culture for Genetic Testing, Amniotic Fluid or CULFB / Fibroblast Culture for Molecular Testing, Chorionic Villi/Products of Conception so that cultures may be set up specifically for use in these tests.

Shipping Instructions

Advise Express Mail or equivalent if not on courier service.

Necessary Information

1. 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.

2. Notify the laboratory if the pregnancy involves an egg donor or gestational carrier.

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

Submit only 1 of the following specimens:

 

Supplies: CVS Media (RPMI) and Small Dish (T095)

Specimen Type: Chorionic villi

Container/Tube: 15-mL tube containing 15-mL of transport media

Specimen Volume: 20-30 mg

Collection Instructions:

1. Collect specimen by the transabdominal or transcervical method.

2. Transfer chorionic villi to a Petri dish containing transport medium (Such as CVS Media [RPMI] and Small Dish).

3. Using a stereomicroscope and sterile forceps, assess the quality and quantity of the villi and remove any blood clots and maternal decidua.

 

Supplies: Refrigerate/Ambient Shipping Box, 5 lb (T329)

Specimen Type: Amniotic fluid

Container/Tube: Amniotic fluid container

Specimen Volume: 20-30 mL

Collection Instructions:

1. Optimal timing for specimen collection is during 14 to 18 weeks of gestation, but specimens collected at other weeks of gestation are also accepted. Provide gestational age at the time of amniocentesis.

2. Discard the first 2 mL of amniotic fluid.

3. Place the tubes in a Refrigerate/Ambient Shipping Box, 5 lb.

4. Fill remaining space with packing material.

Additional Information:

1. Unavoidably, about 1% to 2% of mailed-in specimens are not viable.

2. Bloody specimens are undesirable.

3. Results will be reported and also telephoned or faxed, if requested.

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 Prenatal Patient Information (T716)

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

Amniotic Fluid: 12 mL

Chorionic Villi: 12 mg; If ordering in conjunction with other testing: If ordered with PADF: 14 mL or 14 mg; with CHRAF: 24 mL; with CHRCV: 24 mg; with PADF and CHRAF/CHRCV: 26 mL or 26 mg

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
Varies Refrigerated (preferred)
Ambient

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

Prenatal diagnosis of copy number changes (gains or losses) across the entire genome

 

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

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

Cultures from this specimen will be discarded 10 days after all cytogenetic test results have been reported. If further testing is desired, call the laboratory at 800-533-1710.

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

Maternal cell contamination (MCC) testing will be performed at no additional charge if a maternal blood sample is received to rule out the presence of maternal cells in the prenatal sample, see Additional Testing Requirements.

 

If an insufficient sample is received or MCC is identified in the prenatal sample, microarray testing will be performed on cultured material.

 

For more information see Prenatal Aneuploidy Screening and Diagnostic Testing Options

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

Chromosomal abnormalities cause a wide range of disorders associated with birth defects and intellectual disability. Many of these disorders can be diagnosed prenatally by analysis of chorionic villi or amniocytes.

 

The most common reasons for performing cytogenetic studies for prenatal diagnosis include advanced maternal age, abnormal prenatal screen, a previous child with a chromosome abnormality, abnormal fetal ultrasound, or a family history of a chromosome abnormality. 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. The American College of Obstetricians and Gynecologists and the Society for Maternal-Fetal Medicine recommend the chromosomal microarray as a replacement for the fetal karyotype in patients with a pregnancy demonstrating one or more major structural abnormalities on ultrasound when undergoing invasive prenatal diagnosis.(1)

 

This CMA test utilizes more than 1.9 million copy number probes and approximately 750,000 single nucleotide polymorphism probes for the detection of copy number changes and regions with absence of heterozygosity. Identification of regions of excessive homozygosity on a single chromosome could suggest uniparental disomy, which may warrant further clinical investigation when observed on chromosomes with known imprinting disorders. In addition, the detection of excessive homozygosity on multiple chromosomes may suggest consanguinity.

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

Copy number variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

 

When interpreting results, it is important to realize that 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 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).(2) Copy number changes with unknown significance will be reported when at least one protein-coding gene is involved in a deletion greater than 1 megabase (Mb) or a duplication greater than 2 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. Regions with absence of heterozygosity (AOH) of unknown significance will be reported when greater than 5 Mb (terminal) and 10 Mb (interstitial) on UPD-associated chromosomes. Whole genome AOH will be reported when greater than 5% 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.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

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

 

This test is not designed to detect low-level 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.

Supportive Data

The array was validated by testing 40 prenatal specimens (direct and cultured amniotic fluid and chorionic villus samples) previously tested using chromosome analysis, fluorescence in situ hybridization (FISH) analysis, or a polymerase chain reaction (PCR)-based assay. All abnormalities previously identified by another methodology were confirmed.

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

1. American College of Obstetricians and Gynecologists Committee on Genetics. Committee opinion no. 581: the use of chromosomal microarray analysis in prenatal diagnosis. Obstet Gynecol. 2013 Dec;122(6):1374-1377. doi: 10.1097/01.AOG.0000438962.16108.d1

2. 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 Feb;19(2):249-255. doi: 10.1038/gim.2016.190

3. Wapner RJ, Martin CL, Levy B, et al: Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 2012 Dec;367(23):2175-2184. doi: 10.1056/NEJMoa1203382

4. Armengol L, Nevado J, Serra-Juhe C, et al: Clinical utility of chromosomal microarray analysis in invasive prenatal diagnosis. Hum Genet. 2012 Mar;131(3):513-523. doi: 10.1007/s00439-011-1095-5

5. Breman A, Pursley AN, Hixson P, et al: Prenatal chromosomal microarray analysis in a diagnostic laboratory; experience with >1000 cases and review of the literature. Prenat Diagn. 2012 Apr;32(4):351-361. doi: 10.1002/pd.3861

6. South ST, Lee C, Lamb AN, et al: ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: Revision 2013. Genet Med. 2013 Nov;15(11):903-909. doi: 10.1038/gim.2013.129

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 amniotic fluid or chorionic villus sample 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, 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.

10 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

Amniotic Fluid: Any remaining supernatant or whole fluid aliquots are discarded 14 days after results are reported. Chorionic Villi: Any remaining specimen is discarded at the time results are reported.

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
CMAP Chromosomal Microarray, Prenatal 86611-1
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.
54714 Result Summary 50397-9
54715 Result 62356-1
54716 Nomenclature 62356-1
54717 Interpretation 69965-2
CG900 Reason For Referral 42349-1
CG780 Specimen 31208-2
54718 Source 31208-2
54719 Method 85069-3
53422 Additional Information 48767-8
54720 Released By 18771-6

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 | Create a 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