Chromosomal Microarray, Autopsy, Products of Conception, or Stillbirth (CMAPC)

Test Code: CMAPCSO

Overview
Ordering
Specimen
Performing
Clinical/Interpretive
Contacts
Coding

Synonyms/Keywords

Array CGH
Oligonucleotide Array
Oligo Array
Single Nucleotide Polymorphism (SNP) Array
Whole Genome Array
Fetal Demise
Miscarriage
Pregnancy Loss
aCGH (Array Comparative Genomic Hybridization)
CMAMT

Chromosomal Microarray, Autopsy, Products of Conception, or Stillbirth, Varies

Chromosomal Microarray, POC

TI CMAPCSO

Useful For

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

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 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

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

Specimen Requirements

Specimen Type	Preferred Container/Tube	Acceptable Container/Tube	Specimen Volume	Specimen Minimum Volume (allows for 1 repeat)
Products of conception or stillbirth	Sterile container with sterile Hank's solution (T132), Ringer's solution, or normal saline	While fresher specimens prepared as described are preferred, analysis can be attempted on specimens that have been in less-than-ideal conditions	1 cm(3) of placenta (including 50-mg chorionic villi) and 1 cm(3) biopsy specimen of muscle/fascia from the thigh	Muscle-Fascia: 1 cm(3)
Autopsy	Sterile container with sterile Hank's solution (T132), Ringer's solution, or normal saline		1 cm(3) biopsy specimen of muscle/fascia from the thigh	Muscle-Fascia: 1 cm(3)
Amniotic Fluid	Amniotic Fluid Container		20-30 mL
Chorionic villus	15-mL tube containing 15 mL of transport media		50 mg	10 mg

Collection Processing Instructions

NOTE: A maternal blood sample is requested when ordering this test; maternal blood is desired, but not required for testing. Order Marshfield Labs Testcode PPAPSO, Parental Sample Prep for Prenatal Microarray Testing.

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.

Products of conception or stillbirth:

Do not send entire fetus.

Autopsy:

1. Wash biopsy site with an antiseptic soap.

2. Thoroughly rinse area with sterile water.

3. Do not use alcohol or iodine preparations.

4. Biopsy specimens are best taken by punch biopsy to include full thickness of dermis.

Amniotic Fluid:

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 Mailer, 5 lb (T329).

4. Fill remaining space with packing material.

Chorionic villus:

1. Collect chorionic villus specimen (CVS) by transabdominal or transcervical method.

2. Transfer CVS to a Petri dish containing transport medium (Such as CVS Media (RPMI) and Small Dish [T095]).

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

Specimen Stability Information

Specimen Type	Temperature
All Types	Ambient (preferred)
All Types	Refrigerate

Rejection Criteria

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Performing Laboratory Information

Performing Location	Day(s) Test Performed	Report Available	Methodology/Instrumentation
Mayo Clinic Laboratories	Monday through Friday	21 to 30 days	Chromosomal Microarray

Reference Lab

Mayo Clinic Laboratories

Reference Range Information

Interpretive Report

Interpretation

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 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 10% 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.

Outreach CPTs

CPT	Modifier (if needed)	Quantity	Description	Comments
81229		1