Chromosomal Microarray (CytoScan HD 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® HD assay provides a genome-wide approach that enables high-resolution DNA copy number analysis to detect gains, losses, loss of heterozygosity (LOH), regions identical by descent, and uniparental disomy (UPD) on a single array1.

Clinical Background

The ability of chromosomal microarray to detect submicroscopic genomic abnormalities has revolutionized the clinical diagnostic approach to individuals with genetic conditions. Over the past decade, many pivotal advances in the understanding of the genetics of hematologic diseases have emerged from SNP array analysis. SNP arrays afford useful platforms for discovering disease alleles that can shed new light on the pathobiology of leukemias and other hematologic malignancies2-5. Microarray technology is prenatal diagnosis is emerging and promises higher sensitivity for detecting genomic abnormalities in fetuses with ultrasound abnormalities and other indications2-6.


The CytoScan® HD Assay 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. Mullighan CG et al., Nature 446(137):758-764, 2007.
  3. Delhommeau F et al., New England Journal of Medicine 360(22):2289-2301, 2009.
  4. Langemeijer SM et al., Nature Genetics 41(7):838-842, 2009.
  5. Schwartz S., Clinics in Laboratory Medicine, 31(4):581-594, 2011.
  6. Schaaf et al., The Annual Review of Genomics and Human Genetics 12:25-51, 2011.