Testing on fetal and/or placental tissue from products of conception, stillbirth, or autopsy. See information on specimen requirements and billing below.



Chromosomal microarray (CMA) is a molecular cytogenomic tool for detecting both copy number changes (deletions and duplications) and copy-neutral regions of homozygosity (ROH) within the DNA.  


Indications for Pregnancy Loss CMA

  • Spontaneous pregnancy loss
  • Pregnancy termination due to anomalies
  • Intrauterine Growth Restriction
  • Stillbirth/Neonatal death


Test Uses

Chromosome SNP microarray can be utilized for detection of the following genomic changes:

  • Copy Number Variants (CNV) – duplications or deletions of chromosomal material
    • Pathogenic and Likely Pathogenic are always reported
    • Variants of Uncertain Significance (VUS) are reported if they meet the reportable size threshold
    • Benign and Likely Benign are not reported
  • Regions of Homozygosity (ROH) – areas of identical DNA
    • ROH is not diagnostic but may narrow down areas and/or autosomal recessive genes of interest to direct further molecular testing for a patient
    • Shared ancestry/identity by descent is more likely when 2% or more of the genome is identical. Close consanguinity is predicted when 10% or more of the genome is identical
    • Uniparental Isodisomy is detectable by SNP array while heterodisomy is not. Additional testing for imprinted disorders may be recommended
  • Mosaicism of a second cell line down to ~20%
  • CNV pathogenicity is determined according to Riggs, et al. 

Follow-Up Studies

CGL often recommends follow-up studies to further elucidate positive microarray results. Recommendations, if any, appear in the proband’s result report. Follow-up testing may include:

  • proband and/or parent karyotype to evaluate for a chromosome rearrangement
  • parental and/or family member testing for the CNV detected
    • When a VUS is detected, two family members can be tested by CGL without additional charge
  • Proband molecular, methylation, or biochemical testing of a gene or region of interest


CMA will NOT detect balanced rearrangements (i.e. inversions, translocations, etc.), heterodisomy, or low-level mosaicism (below ~20%). It will not detect single gene point mutations or small duplications/deletions. CNVs that are smaller than the resolution of the array may not be detected or reported.

SNP CMA may reveal whole genome mosaicism suggestive of presence of two different genomes, as in the case of maternal cell contamination.  The presence of maternal cell contamination may limit the interpretation of CMA results.  For products of conception or placenta, when a single female genome is detected, it is assumed to represent the female fetus.  However, the rare possibility that the DNA analyzed has originated in the gestational carrier cannot be excluded; GCC testing is required to rule out this possibility.


Reporting Thresholds

FindingReportable Size
Loss/Deletion 1 Mb or larger
Gain/Duplication 2 Mb or larger
Region of Homozygosity 10 Mb or larger, 3 Mb and larger analyzed*

*Smaller ROH or copy number variants may be reported if demonstrated to have high clinical value.


Information/Patient Forms

CMA Consent: (English, Spanish)

Pregnancy Loss Microarray Clinical Information Form​

Billing Waiver for Microarray*

*Patients without a preauthorization for CMA who are denied coverage by their insurance provider may be liable for the entire cost of the CMA if the Billing CMA Waiver is not signed. A signed waiver will reduce the fee by 40% if denied coverage.

Chromosome analysis is performed on G-banded metaphase chromosomes for the purpose of detecting numerical and/or structural abnormalities that may be present. These include aneuploidy (such as trisomy or monosomy), mosaicism, unbalanced rearrangements such as interstitial or terminal deletions/duplications and/or balanced rearrangements such as translocations and inversions.


  • Suspicion of aneuploidy
  • Congenital anomalies
  • Intrauterine growth restriction
  • Stillbirth or neonatal death
  • Family history of chromosome abnormality


For standard chromosome analysis, 15 cells are counted and 5 cells are analyzed for chromosome structure and number with at least 400-450 band level of resolution.


Duplications or deletions smaller ~5 Mb are not detectable by chromosome analysis. Chromosome analysis cannot detect Uniparental Disomy, Regions of Homozygosity (ROH), or single gene conditions.

Follow-up Testing

Some chromosome abnormalities may warrant additional testing by microarray including unbalanced rearrangements, apparently balanced rearrangements in an individual with symptoms, and copy number variants to determine the extent of chromosome material involved and identify affected genes. Testing for family members may also be recommended when a chromosome rearrangement is identified.

**Please note: Chromosome analysis is only possible on living cells because cell culture is needed. An extended amount of time between fetal demise and arrival of the sample at the lab will increase the likelihood of test failure. Addition of concurrent or reflex chromosomal microarray (CMA) testing will significantly improve the chance of reportable results.

Fluorescence in situhybridization (FISH) detects chromosome copy number changes. Pregnancy Loss Trisomy FISH probes for chromosomes anomalies often seen in products of conception include X, Y, 13, 15, 16, 18, 21, and 22.


  • Pregnancy loss
  • Fetal anomalies
  • Intrauterine growth restriction
  • Stillbirth or neonatal death
  • Family history of chromosome abnormality


FISH is not considered a diagnostic test and cannot determine the extent of material duplicated or deleted. Diagnostic testing by chromosome analysis or chromosome microarray (CMA) is required for confirmation.


This test has historically been known as "Maternal Cell Contamination" (MCC) analysis.


Various methods of prenatal sample collection pose an increased risk for contamination with gestational carrier cells including CVS, products of conception, and other placental samples.  Such contamination can result in ambiguous or even unusable results if not clarified. When not excluded by other test results, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) recommend that GCC studies be performed to optimize interpretation of the primary study molecular and/or cytogenetic results.



  • Placental or early POC samples
  • Samples of uncertain tissue origin




GCC testing by short tandem repeat (STR) analysis is performed by Colorado Molecular Correlates (CMOCO), a partner lab of Colorado Genetics Laboratory (CGL). 

Gestational carrier contamination studies are performed as needed depending on the specimen provided. GCC studies are typically run concurrently with chromosome microarray, and as a reflex analysis if XX or mosaic XX results are found in the proband sample. The decision when and if to run GCC analysis will be made by CGL in conjunction with the ordering provider.


For additional information, contact CGL Client Services at (303)724-5701.

A blood or buccal sample from the carrier of the pregnancy is required for GCC testing and may be submitted along with tissue sample. 

Acceptable Samples Unacceptable Samples
Send 1 cm3 of any of the following samples: Samples will be mailed back without testing:
·         Placenta from cord insertion site
·         Fetal tissue from gonad, kidney, lung, or fascia lata
·         Umbilical cord ONLY when under 16 weeks for microarray
·         Intact fetuses over 10 weeks gestation
·         Large fetal parts
·         Samples preserved in formalin/formaldehyde
·         Surgical equipment used for termination, etc.


Collection Instructions

All samples must be labeled with the patient’s name and second identifier (ex: DOB, MRN).

  1. Collect aseptically in sterile plastic screw-top tube/container filled with sterile transport media or sterile saline solution. Transport media is available upon request.
  2. Label container with patient's name and second identifier (e.g. DOB).
  3. If sending both fetal and placental specimens (recommended), send in separate containers and label each container with specimen type. Both samples will be tested under one charge.
  4. Store at room temperature, refrigerate if overnight.


Chromosome analysis and/or CMA 1 cm3 tissue (see acceptable tissue list) Chromosomes: 88233, 88262, 88280, 88291
CMA: 88233, 81229
Pregnancy Loss Trisomy FISH (part of reflex pathway with chromosomes or CMA) No additional sample needed 88271 x 9, 88274 x 4, 88291
Gestational Carrier Contamination Testing Peripheral Blood: 3 ml in EDTA tube
Buccal Swab*
Sample must be from the gestational carrier.
Billed by outside lab.

*Buccal swab kits available by request.



  1. American College of Obstetricians and Gynecologists. Committee Opinion No. 581: The use of chromosomal microarray analysis in prenatal diagnosis. Obstet Gynecol. 122:1374–7, 2013.
  2. Kearney HM, et al. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 13:680-5, 2011.
  3. Nagan N, Faulkner NE, Curtis C, Schrijver I.  Laboratory guidelines for detection, interpretation and reporting of maternal cell contamination in prenatal analyses. J Mol Diagn. 2011; 13(1):7-11.
  4. Riggs ER, et al. Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med. 2020;22:245-257. Erratum in: Genet Med. 2021;23:2230.
    1. South ST, et al. ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013. Genet Med. 15:901-9, 2013.
    2. Wapner RJ, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 367:2175-84, 2012.
    3. Reddy UM, et al., Karyotype versus Microarray Testing for Genetic Abnormalities after Stillbirth. The New England Journal of Medicine 367:23:2185-2193, 2013.

    Colorado Genetics Laboratory (SOM)

    CU Anschutz

    Bioscience 2

    12705 East Montview Boulevard

    Suite 400

    Aurora, CO 80045


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