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26013 Chromosomal Microarray, Autopsy, Products of Conception, or Stillbirth (CMAPC)

Chromosomal Microarray, Autopsy, Products of Conception, or Stillbirth (CMAPC)
Test Code: CMAPCSO
Synonyms/Keywords

​​Accel, aCGH, array CGH, Array Comparative Genomic Hybridization), CMAMT, Constitutional Array, CytoScan, Fetal Demise​, Microarray, Molecular Karyotype, MiscarriageOligo Array, Oligonucleotide Array, Pregnancy LossSingle Nucleotide Polymorphism (SNP) ArrayWhole Genome Array, POC

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

NECESSARY INFORMATION:

Provide a reason for testing 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.

Notify the laboratory if the pregnancy involves an egg donor or gestational carrier.nd maternal decidua.

Specimen Requirements
Specimen Type Preferred Container/Tube Acceptable Container/Tube Specimen Volume Specimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no 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 (see PPAP / Parental Sample Prep for Prenatal Microarray Testing, Blood). Testing will not be rejected if maternal blood is not received; however, the possibility of maternal cell contamination cannot be excluded. 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, Blood.

Products of conception (POC) or stillbirth:
1.  Attempt to identify and send only fetal tissue for analysis.
2.  If a fetus cannot be specifically identified, collect 50-mg villus material or tissue that appears to be of   fetal origin.
3.  If multiple specimen types are sent, send each specimen in a separate container.  Multiple specimens received (eg, placenta and fetal thigh) will be ordered under 1 test.  All specimens will be processed separately.  
Additional Information:
1. Do not send entire fetus.
2. While fresher specimens prepared as described above are preferred, we can attempt analysis on specimens that have been in less-than-ideal conditions.

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.

Specimen Stability Information
Specimen Type Temperature
​All Types ​ ​Ambient (preferred)
​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 Sunday
​10 to 25 days Chromosomal Microarray (CMA)
Reference Lab
Test 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, a stillborn infant, or neonate (autopsy) may provide useful information concerning the cause of 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.

Chromosomal microarray 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 2 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 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 Range Information

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.

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
Synonyms/Keywords

​​Accel, aCGH, array CGH, Array Comparative Genomic Hybridization), CMAMT, Constitutional Array, CytoScan, Fetal Demise​, Microarray, Molecular Karyotype, MiscarriageOligo Array, Oligonucleotide Array, Pregnancy LossSingle Nucleotide Polymorphism (SNP) ArrayWhole Genome Array, POC

Ordering Applications
Ordering Application Description
​Cerner​Chromosomal Microarray, POC
If the ordering application you are looking for is not listed, contact your local laboratory for assistance.
Specimen Requirements
Specimen Type Preferred Container/Tube Acceptable Container/Tube Specimen Volume Specimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no 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

NOTE:  A maternal blood sample is requested when ordering this test (see PPAP / Parental Sample Prep for Prenatal Microarray Testing, Blood). Testing will not be rejected if maternal blood is not received; however, the possibility of maternal cell contamination cannot be excluded. 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, Blood.

Products of conception (POC) or stillbirth:
1.  Attempt to identify and send only fetal tissue for analysis.
2.  If a fetus cannot be specifically identified, collect 50-mg villus material or tissue that appears to be of   fetal origin.
3.  If multiple specimen types are sent, send each specimen in a separate container.  Multiple specimens received (eg, placenta and fetal thigh) will be ordered under 1 test.  All specimens will be processed separately.  
Additional Information:
1. Do not send entire fetus.
2. While fresher specimens prepared as described above are preferred, we can attempt analysis on specimens that have been in less-than-ideal conditions.

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.

Specimen Stability Information
Specimen Type Temperature
​All Types ​ ​Ambient (preferred)
​Refrigerate
Rejection Criteria
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.
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

NECESSARY INFORMATION:

Provide a reason for testing 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.

Notify the laboratory if the pregnancy involves an egg donor or gestational carrier.nd maternal decidua.

Reference Range Information

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.

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. 

For more information visit:
Performing Laboratory Information
Performing Location Day(s) Test Performed Report Available Methodology/Instrumentation
​Mayo Clinic Laboratories Monday through Sunday
​10 to 25 days Chromosomal Microarray (CMA)
Reference Lab
For billing questions, see Contacts
Outreach CPTs
CPT Modifier
(if needed)
Quantity Description Comments
​81229 ​1
For most current information refer to the Marshfield Laboratory online reference manual.