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Test ID: CMAMT Chromosomal Microarray, Autopsy/Products of Conception/Stillbirth, Tissue

Useful For

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 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

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. If additional FISH testing is requested, it will be performed at an additional charge.

 

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

 

Maternal cell contamination (MCC) 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. 

 

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

Method Name

Chromosomal Microarray (CMA) using Affymetrix Oncoscan 

Reporting Name

Chromosomal Microarray, POC, FFPE

Specimen Type

Varies


Additional Testing Requirements


A maternal blood sample is requested when ordering this test. A paternal blood sample is desired but not required. See PPAP / Parental Sample Prep for Prenatal Microarray Testing (PPAP must be ordered under a different order number than the prenatal specimen).



Necessary Information


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.



Specimen Required


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.

 

Specimen Type: Slides

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


Specimen Minimum Volume

Formalin-fixed paraffin-embedded tissue block or 5 consecutive unstained tissue sections cut at 5 microns placed on positively charged microscope slides and 1 hematoxylin and eosin-stained slide

Specimen Stability Information

Specimen Type Temperature Time
Varies Ambient (preferred)
  Refrigerated 

Clinical Information

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. Identification of regions of excess homozygosity on a single chromosome could suggest uniparental disomy that may warrant further clinical investigation when observed on chromosomes with known imprinting disorders. In addition, the detection of excess homozygosity on multiple chromosomes may suggest consanguinity.

Reference Values

An interpretive report will be provided.

Interpretation

Copy number variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. A normal result will be reported as arr(1-22,X)x2 or arr(1-22)x2,(XY)x1. A copy number change known to be of clinical significance will be reported as pathogenic. Copy number changes with unknown significance will be reported as either likely benign, uncertain, or likely pathogenic. Absence of heterozygosity will be reported.

 

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.

 

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.

 

The detection of excess homozygosity may suggest the need for additional clinical testing to confirm uniparental disomy or to test for mutations in genes associated with autosomal recessive disorders present in regions of homozygosity.

Clinical Reference

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;122:1374-1377
2. Wapner RJ, Martin CL, Levy B, et al: Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012;367:2175-2184

3. 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
4. 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

5. 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

Day(s) and Time(s) Performed

Samples processed Monday through Sunday. Results reported Monday through Friday, 8 a.m.-5 p.m.

Analytic Time

21 days

Test Classification

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 U.S. Food and Drug Administration.

CPT Code Information

81229

LOINC Code Information

Test ID Test Order Name Order LOINC Value
CMAMT Chromosomal Microarray, POC, FFPE In Process

 

Result ID Test Result Name Result LOINC Value
44005 Result Summary 50397-9
44006 Result 62356-1
44007 Nomenclature 55107-7
44008 Interpretation 69965-2
44009 Reason for Referral 42349-1
44010 Specimen 31208-2
44011 Source 31208-2
44012 Tissue ID No LOINC Needed
44013 Method 49549-9
44014 Additional Information 48767-8
44015 Disclaimer 62364-5
44016 Released By No LOINC Needed

Forms

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

2. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

Mayo Medical Laboratories | Genetics and Pharmacogenomics Catalog Additional Information:

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