Test Catalog

Test Id : CMAMT

Chromosomal Microarray, Autopsy/Products of Conception/Stillbirth, Tissue

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

Diagnosis of congenital copy number changes in products of conception, including aneuploidy (ie, trisomy or monosomy) and structural abnormalities

 

Diagnosing chromosomal causes for fetal death

 

Determining recurrence risk of future pregnancy losses

 

Determining the size, precise breakpoints, gene content, and any unappreciated complexity of abnormalities detected previously 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

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

Hematoxylin and eosin stain review of the paraffin-embedded sample is performed to identify the area of fetal tissue prior to DNA extraction and microarray analysis.

 

See Frequently Asked Questions: Cytogenetic Testing of Products of Conception by Chromosomal Microarray Analysis

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, POC, FFPE

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

OncoScan

Congenital Array

Constitutional Array

Absence of Heterozygosity (AOH)

Fetal Demise

Miscarriage

Pregnancy Loss

Paraffin Embedded Tissue Array

Paraffin Embedded POC Array

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

Hematoxylin and eosin stain review of the paraffin-embedded sample is performed to identify the area of fetal tissue prior to DNA extraction and microarray analysis.

 

See Frequently Asked Questions: Cytogenetic Testing of Products of Conception by Chromosomal Microarray Analysis

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

If a fresh tissue specimen is submitted, this test will be cancelled and CMAPC / Chromosomal Microarray, Autopsy, Products of Conception, or Stillborn, Varies will be added and performed as the appropriate test.

Additional Testing Requirements

A maternal blood sample is requested when ordering this test; order PPAP / Parental Sample Prep for Prenatal Microarray Testing, Blood under a different order number than the prenatal specimen. Maternal cell contamination testing will be performed at no additional charge on the maternal blood and fetal tissue to rule out the presence of maternal cells in the product of conception sample. Testing will not be rejected if maternal blood is not received; however, the possibility of maternal cell contamination cannot be excluded.

 

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

Necessary Information

A reason for referral and pathology report are required in order for testing to be performed. Send information with specimen. Acceptable pathology reports include working drafts, preliminary pathology or surgical pathology reports.

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
CG975 Reason For Referral

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:

 

Specimen Type: Tissue

Container/Tube: Formalin-fixed, paraffin-embedded block containing fetal or placental (including chorionic villi) tissue.

Additional Information: A pathology report and reason for referral must be submitted 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.

 

Specimen Type: Slides

Specimen Volume: 6 Consecutive, unstained, 5-micron-thick sections placed on positively charged slides and 1 hematoxylin and eosin-stained slide.

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 in Special Instructions:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Chromosomal Microarray Prenatal Patient Information (T716) in Special Instructions.

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

Formalin-fixed, paraffin-embedded tissue block

5 Consecutive, unstained slides and 1 hematoxylin and eosin-stained slide

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 Ambient (preferred)
Refrigerated

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

Diagnosis of congenital copy number changes in products of conception, including aneuploidy (ie, trisomy or monosomy) and structural abnormalities

 

Diagnosing chromosomal causes for fetal death

 

Determining recurrence risk of future pregnancy losses

 

Determining the size, precise breakpoints, gene content, and any unappreciated complexity of abnormalities detected previously 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

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

Hematoxylin and eosin stain review of the paraffin-embedded sample is performed to identify the area of fetal tissue prior to DNA extraction and microarray analysis.

 

See Frequently Asked Questions: Cytogenetic Testing of Products of Conception by Chromosomal Microarray Analysis

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

Chromosomal abnormalities may result in malformed fetuses, spontaneous abortions, or neonatal deaths. Estimates of the frequency of chromosome abnormalities in spontaneously aborted fetuses range from 15% to 60%.

 

Chromosomal microarray (CMA) studies of products of conception (POC), a stillborn infant, or a neonate (autopsy) may provide useful information concerning the cause of miscarriage or fetal loss. In addition, CMA may provide information regarding the recurrence risk for future pregnancy loss and risk of having subsequent children with chromosome anomalies. This is particularly useful information if there is a family history of 2 or more miscarriages or when fetal malformations are evident.

 

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 over 220,000 markers for the detection of copy number changes and regions with absence of heterozygosity. The detection of excess homozygosity on multiple chromosomes may suggest consanguinity. Homozygosity involving the entire genome is indicative of a complete molar pregnancy.

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.

 

While many 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, making interpretation of these variants challenging. In these situations, a number of considerations are taken into account to help interpret results including the size and gene content of the imbalance, as well as whether the change is a deletion or duplication. Parental testing may also be necessary to further assess the potential pathogenicity of a copy number change. In such situations, the inheritance pattern and clinical and developmental history of the transmitting parent will be taken into consideration.

 

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 1 megabase (Mb) or a duplication greater than 2 Mb.

 

The detection of excessive homozygosity may suggest the need 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. Homozygosity will be reported when involving greater than 20% of the genome. Homozygosity involving the entire genome is indicative of a complete molar pregnancy. 

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 balanced chromosome rearrangements such as Robertsonian or other reciprocal translocations, inversions, or balanced insertions.

 

 

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 unrelated 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 25 formalin-fixed, paraffin-embedded products of conception specimens previously tested using fluorescence in situ hybridization analysis. All abnormalities previously identified by another methodology 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. 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;122:1374-1377

3. Wapner RJ, Martin CL, Levy B, et al: Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 2012;367:2175-2184

4. Armengol L, Nevado J, Serra-Juhe C, et al: Clinical utility of chromosomal microarray analysis in invasive prenatal diagnosis. Hum Genet. 2012;131:513-523

5. Laurino MY, Bennett RL, Saraiya DS, et al: Genetic evaluation and counseling of couples with recurrent miscarriage: recommendations of the National Society of Genetic Counselors. J Genet Couns. 2005;14:165-181

6. Reddy UM, Page GP, Saade GR, et al: Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med. 2012;367:2185-2193

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 paraffin-embedded autopsy, products of conception, or stillbirth samples 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.(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.

21 to 30 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Slides and H and E-stained slide used for analysis are retained by the laboratory. Client provided paraffin blocks and extra unstained slides (if provided) will be returned after testing is complete.

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
CMAMT Chromosomal Microarray, POC, FFPE 94087-4
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.
44005 Result Summary 50397-9
44006 Result 62356-1
44007 Nomenclature 62356-1
44008 Interpretation 69965-2
44009 Reason for Referral 42349-1
44010 Specimen 31208-2
44011 Source 31208-2
44012 Tissue ID 80398-1
44013 Method 85069-3
44014 Additional Information 48767-8
44016 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 | 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

Test Update Resources

Change Type Effective Date
Test Status - Test Resumed 2021-05-06