Chromosomal Microarray (CytoScan Dx Assay)

Test Details

Clinical Significance

A chromosomal microarray can detect chromosomal variations (gain and loss of genomic material) at higher resolution than a routine karyotype.  The CytoScan® Dx Assay is the first FDA-cleared whole genome diagnostic test to aid physicians in identifying the underlying genetic cause of developmental delay, intellectual disability, congenital anomalies, or dysmorphic features in children.  According to American Academy of Neurology, the Child Neurology Society, and the American College of Medical Genetics, a chromosomal microarray analysis is considered the first-line genetic test to aid in the diagnostic evaluation of intellectual disability when patient history and physical examination do not provide an obvious clinical diagnosis1-4.

Clinical Background

In children, the prevalence of developmental disability is estimated to be 3.87% and occurs across all ethnic, racial and socio-economic groups5. Recent studies have shown that 1 in 33 babies is born with congenital anomalies in the United States6. Frequently, developmental delay and/or intellectual disability is present with one or more congenital anomalies of dysmorphic features.  Early intervention is key to providing better outcomes for children with special needs.  Establishing underlying genetic diagnosis early can provide physicians and families with knowledge of which disorder is affecting the child, prognosis and comorbidity information, all of which have significant implications for both the physicians and the family.


The CytoScan® Dx Assay, the FDA-cleared and CE marked post natal blood test involves DNA extraction, hybridization to microarray containing 2.69 million functional markers across the entire genome, thus ensuring all genes are represented.  The markers contain both copy number and single nucleotide polymorphism probes, thus permitting elucidation of both allelic imbalances and loss of heterozygosity/absence of heterozygosity (LOH/AOH), both of which increase the risk of recessive disorders.  Data analysis is done by American Society of Clinical Pathology (ASCP) certified technologists with final interpretation by American Board of Medical Genetics certified laboratory director.

Interpretation of Results

The morphologic interpretation and correlation of results on all cases is performed by a board-certified doctoral level scientist (laboratory director). The final report identifies the chromosomal sex and if any genomic imbalances detected.  If abnormalities are present, they are explained in a paragraph which helps to clarify and correlate clinical findings with pathological morphology. Further testing (parental studies, additional molecular/FISH studies) is recommended to support or confirm chromosome aberrations or when inconclusive results are found.  References are included in the report to help the referring physician with interpretation, which include books or journals that contain appropriate information.


  2. Michelson DJ et al., Neurology 77(17):1629-1635, 2011.
  3. Miller DT et al., American Journal of Human Genetics 86(5):749-764, 2010.
  4. Manning M and Hudgins L., Genetics in Medicine 12(11):742-745, 2010.
  5. Boyle CA et al., Pediatrics 127(6):1034-1042, 2011.
  6. Heron MP et al., National Vital Statistics Reports 57(14):1-136, 2009.