Testing on prenatally collected samples of ongoing pregnancies. 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 Prenatal CMA

  • Abnormal ultrasound: structural anomalies or markers
  • Abnormal NIPS result confirmation
  • Family history of chromosome abnormality or copy number variant


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 parental 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.

CMA may reveal whole genome mosaicism suggestive of the presence of two different genomes, as in the case of contamination with cells from the gestational carrier (GCC), which may limit the interpretation of CMA results.  For products of conception, placenta or chorionic villi samples, 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)

Prenatal Microarray Clinical Information Form​

Billing Waiver for Microarray*

*Patients without a preauthorization for CMA who are denied coverage by their insurance provider will 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.


Standard (Routine) Chromosome Analysis

  • Increased risk of aneuploidy due to advanced maternal age or abnormal screening
  • Positive or ambiguous NIPS results
  • Congenital anomalies on ultrasound
  • Intrauterine growth restriction
  • Family history of chromosome abnormality

 5-cell Chromosome Analysis

  • As a supplement to Chromosomal Microarray (CMA) studies, five cells are evaluated to identify or rule out balanced chromosome rearrangements for the indications above. Not a stand-alone test.


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.


Fluorescence in situ hybridization (FISH) detects chromosome aneuploidy and submicroscopic genomic copy number changes such as deletions and duplications in specific regions.


  • Suspicion of aneuploidy (X, Y, 13, 18, 21)
  • Sex determination (if discordant/ambiguous, includes X, Y, SRY locus)
  • Suspicion for specific disorders:
    • Williams Syndrome 7q11.2
    • Prader-Willi/Angelman Syndrome 15q11.2
    • DiGeorge Spectrum 22q11.2
    • X-linked Ichthyosis Xp22.21
  • Suspicion for other known microduplication/deletion syndromes (see Fish Probe List)
  • Familial testing after diagnosis of proband


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 is required. See ordering options below.

Occasionally, FISH may be recommended to clarify the results of chromosome analysis or microarray. Such additional recommendations will be discussed with the ordering provider prior to being performed.




This test has historically been known as "Maternal Cell Contamination" 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 prenatal sample. 


Amniotic fluid alpha-fetoprotein (AF-AFP) testing at 15-30 weeks gestation screens a fetus for an increased risk of open neural tube or open body wall defects. AF-AFP analysis can be used to further evaluate abnormal serum AFP levels identified during maternal serum screening. Acetylcholinesterase (AChE) testing is performed as a reflex confirmation test on individuals with an abnormal amniotic fluid alpha-fetoprotein (AF-AFP) level of 2.0 multiples of the mean (MOM) or greater.


  • Increased risk for neural tube defects by ultrasound or serum screening
  • Increased risk for body wall defects by ultrasound or serum screening
  • Routine rule-out of neural tube or body wall defects when other prenatal screening is ordered


AF-AFP testing is performed by the Associated Regional University Pathologists, Inc. (ARUP).  Results and interpretation of the AChE are provided to the Colorado Genetics Laboratory by Associated Regional University Pathologists, Inc. (ARUP) and the Foundation for Blood Research (FBR).


afAFP and AChE testing cannot be performed on a chorionic villi sample and require an amniotic fluid sample between 15-30 weeks gestation. Positive/abnormal results from this testing are not specific to a certain genetic or physical diagnosis, but contribute to the overall clinical likelihood of a disorder.




  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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