Germline testing for pediatric and adult individuals. 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.  



ACMG recommends CMA as the first-tier test for individuals with:

  • Unexplained developmental delay
  • Intellectual disability
  • Autism spectrum disorder
  • Congenital anomalies.
  • Other neurological or developmental disorders, such as seizures
  • Family history of a 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 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 for free
  • 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.

Reporting Thresholds

Finding Reportable Size*
Loss/Deletion 200 Kb or larger
Gain/Duplication 400 Kb 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 a high clinical suspicion.



Information/Patient Forms

CMA Consent (English, Spanish)

Postnatal 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.


Family members of probands identified with a copy number variant of potential clinical significance may wish to be tested for this variant as well. When done on a parent, the results may help clarify the pathogenicity of an uncertain finding and/or inform the recurrence risk for other offspring. When performed on a sibling, the results may be diagnostic without requiring a full array analysis.

Targeted microarray results will be analyzed at only the locus/loci of interest. Other findings will not be reported unless obviously pathogenic.

Two family members may receive a targeted CMA without charge if a proband is found to have a Variant of Uncertain Significance (VUS).


Information/Patient Forms

CMA Consent (English, Spanish)

Postnatal 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.


Standard Chromosome Analysis

  • Suspicion of aneuploidy
  • Congenital anomalies
  • Growth delay
  • Intellectual disabilities
  • Infertility
  • Personal or family history of recurrent miscarriage

High-Resolution Chromosome Analysis

  • Known family history of a translocation or other rearrangement
  • Genetic studies (such as microarray) suggestive of a rearrangement

 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, 20 cells are counted and 5 cells are analyzed for chromosome structure and number at the 550 band level of resolution. High-resolution chromosomes are evaluated at a 650 band level. Additional cells (up to 50) are evaluated when mosaicism is suspected.


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 diagnosed proband



FISH is not considered a diagnostic test and cannot determine the extent of material duplicated or deleted. Diagnostic test 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 order provider prior to being performed.




Collection Instructions

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

  • Blood should be collected in a 4ml sodium heparin (green top) tube and stored at room temperature.
  • Buccal swab kits available by request.
  • Skin biopsies should be collected using aseptic technique and placed in a sterile screw-top container with sterile transport media or sterile saline solution. Transport media is available upon request. Label with patient identifiers and tissue type. Store at room temperature or overnight at 4O F.


TestVolumeCPT Codes
Full Chromosome Analysis Peripheral Blood: 4 ml*
Skin Biopsy: 3-4 mm3
Standard: 88230, 88262, 88280, 88291
High-Resolution (not available on skin biopsies): add 88289
Chromosome Microarray Peripheral Blood: 2 ml
Buccal Swab
Skin Biopsy: 3-4 mm3
Full array: 81229
Targeted array: 81479
CMA + 5-cell Chromosome Analysis Peripheral Blood: 4 ml*
Skin Biopsy: 3-4 mm3
81229, 88235, 88230, 88261, 88280, 88291

FISH reflex to chromosomes only or CMA + 5-cell

A positive aneuploidy FISH will be followed by chromosome analysis

A negative aneuploidy FISH will be followed by CMA with 5-cell chromosome analysis

A positive microdup/del FISH will be confirmed as appropriate

Peripheral Blood: 2-3 ml*
Skin Biopsy: 3-4 mm3
Aneuploidy FISH
88271 x 5, 88274 x4, plus chromosomes or CMA codes above
Microdeletion/Duplication FISH
88271 x 2, 88274, 88237, plus chromosomes or CMA codes above
Add 88291 if a chromosome analysis is not performed.

*Please contact the lab if an insufficient blood volume is collected to discuss testing options.



  1. 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.
  2. Miller DT, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 86:749-64, 2010. 
  3. 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. 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.

Colorado Genetics Laboratory (SOM)

CU Anschutz

Bioscience 2

12705 East Montview Boulevard

Suite 400

Aurora, CO 80045


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