Test Overview
Test Methodology

This Chromosomal Microarray (CMA) analysis uses the Illumina CytoSNP-850K array. The Illumina CytoSNP-850K chromosomal microarray uses approximately 850,000 SNPs and oligonucleotide probes to combine genotype and intensity information to detect various types and sizes of structural genomic variation in the human genome. Patient DNA is isolated, linearly amplified, enzymatically fragmented, and hybridized to array probes. Each hybridized array probe is extended with tagged terminating nucleotides. The extended probes are stained, and the array is washed, scanned, and the results are analyzed and interpreted. If a reportable genomic copy number change is detected, a CMA aberration confirmation by rqPCR analysis maybe performed to confirm the array result.

Test Usage

This Chromosomal Microarray (CMA) assay detects copy number changes in genomic DNA. The American College of Medical Genetics (ACMG) recommends chromosomal microarray (CMA) as the first-line genetic test for all children with autism spectrum disorders and other developmental / intellectual disabilities or birth defects (Manning et al. Gene Med 12(11):742-745, 2010). By using CMA testing, a patient’s genomic DNA is examined for gains or losses that are too small to be detected by standard G-banded chromosome studies. The increased resolution of CMA technology over conventional cytogenetic analysis allows for identification of chromosomal imbalances with greater precision, accuracy, and technical sensitivity. Therefore, this CMA assay is a more cost effective alternative to sequential or multiplex FISH for subtelomeric deletions. This CMA assay is used to detect various types and sizes of structural genomic variation in the human genome including deletions, duplications, regions of SNP homozygosity, Uniparental Disomy (UPD), and mosaicism. This CMA analysis is recommended to test patients with Mendelian conditions or syndromes, developmental delays, cognitive impairments, autism spectrum disorders, dysmorphic features, birth defects, congenital anomalies, genomic disorders and germline cancers.

Reference Range *

Interpretive report provided.

Test Limitations

CMA may not detect low-level mosaicism, and cannot detect chromosomal aberrations that do not result in net gains or losses of genomic material, such as balanced chromosomal rearrangements (balanced translocations, balanced insertions, and inversions), rearrangements in repeat sequences (short arms of acrocentric chromosomes and heterochromatic regions), point mutations, indels, and epigenetic alterations. CMA will not detect genomic imbalances in regions that are not represented on the array. Interpretation of CMA results can be complicated by the detection of genomic copy number changes of unknown clinical significance. These copy number variants of unknown clinical significance can be family or population specific and may require further studies, including analysis of parental samples and further medical genetic evaluation. Relative-quantitative PCR (rqPCR) confirmation assay is performed for an aberrant CMA result using a Taqman probe. If two family members have similar rqPCR results, then these results indicate (but do not unequivocally prove) that the two individuals carry the same aberration. For common aneuploidy (e.g., trisomy 21 or trisomy 18) conventional karyotyping may be more appropriate and cost-effective. As well, a single probe FISH assay may be used to confirm a suspected diagnosis of a well-described syndrome, such as DiGeorge or Williams syndromes, as a more cost-effective screening test.

Test Details
Days Set Up
Monday - Friday
Analytic Time

28 days

Soft Order Code
MiChart Code
SNP CMA Analysis (MMGL Chromosomal Microarray)
  • Array CGH (aCGH)
  • Comparative Genomic Hybridization
  • CGH
  • Microarray CGH
  • CMA
  • SNP Array
  • Generic Peds Genetics Test
  • CMAB2
  • CMAB1
  • Array CGH (Post-Natal) Shadow
  • Array CGH 2 (Post-Natal) Shado
  • Chromosomal Microarray Shadow
  • CMAB1S
  • CMAB2S
  • SNP CMA Analysis
  • SNPM1
  • SNPM1S
  • SNP CMA Analysis Shadow
MMGL Molecular Genetics
Specimen Requirements
Collection Instructions

Collect specimen in a lavender top tube. Send intact lavender top tube refrigerated within 24 - 48 hours of collection; specimens MUST be received by the laboratory within 48 hours of collection. Obtaining informed consent from the patient prior to testing is strongly recommended. If desired, a UMHS Request and Consent for Genetic Testing form can be obtained from the MMGL Molecular Genetics Laboratory by contacting the MLabs Client Services Center at 800-862-7284 or online at https://mlabs.umich.edu/sites/default/files/2020-01/file/pci-mmgl_infor….

CMA should not be ordered for phenotypically normal individuals with a family history of a balanced chromosome rearrangement.
Normal Volume
5 - 10 mL EDTA whole blood
Minimum Volume
2 mL EDTA whole blood
Rejection Criteria
Fresh tissue (POC) or paraffin embedded specimens are not acceptable.
Additional Information

Aberrant CMA results will be confirmed by relative-quantitative PCR (rqPCR) when clinically indicated. By ordering this test the clinician acknowledges that additional reflex testing will be performed and billed at a separate additional charge if indicated. Chromosomal Microarray (CMA) analysis is more sensitive than conventional karyotyping. CMA will provide a clinically relevant result in at least 5-17% of individuals with mental retardation and/or developmental problems who have an apparently normal karyotype by conventional cytogenetic analysis (deVries et al., 2005; Shaffer et al., 2006; Krepischi-Santos et al., 2006) and may be able to identify specific loci/genes involved in a genomic imbalance. Test includes pathologist interpretation of results billed as a separate additional charge. By ordering this test the clinician acknowledges that informed consent has been obtained from the patient as required by applicable state or federal laws and the ordering clinician has authorization from the patient permitting MLabs to report the test results to the ordering clinician. Test includes medical geneticist interpretation of results billed as a separate additional charge. This test is not available without interpretation.

CPT Code
Fee Code
Pro Fee CPT
NY State Approved