Cytogenomic Specimen

We offer cytogenomic array as a postnatal first-tier test appropriate for individuals with multiple anomalies that are not specific to well-defined genetic syndromes, apparently non-syndromic developmental delay and/or intellectual disability, or autism spectrum disorders as recommended by the American College of Medical Genetics.

Cytogenomic array is also appropriate for follow-up testing for individuals with the phenotypes listed above with a previously normal chromosome analysis result; clarification of size, precise breakpoints, or gene content of abnormalities detected by routine chromosome analysis or FISH studies; or to rule out cryptic copy number changes (imbalances) at the breakpoints of apparently balanced chromosome rearrangements and for the identification of long, contiguous stretches of homozygosity.

Specimen Requirements

For proper analysis, we require:

  • SNP microarray (shipped at room temperature, avoiding extreme temperatures)
  • 3 mL of blood (NaHep) and 3 mL of blood (EDTA)

Please call our Cytogenetics Laboratory at 773.702.6203 when a specimen has been taken so we can prepare for its delivery and analysis.

No specimens are rejected, but physicians are notified upon receipt of inadequate specimen.

Delivery Instructions

Ship specimens to the Cytogenetics Laboratory as soon as possible after excising them from the patient. Specimens should be delivered to:

Carrie Fitzpatrick, PhD, FACMG
Cytogenetics Laboratory

Room G-712
5841 S. Maryland Ave.
Chicago, IL 60637          

Contact information:
Phone: 773.702.6203
Fax: 773.834.8557

Delivery information should be on the outside of the package.

Test Methods

Cytogenomic SNP array uses the Affymetrix CytoScan HD platform. This array includes 2.67 million markers for copy number (CN) analysis, including approximately 750,000 SNP probes and 1.9 million non-polymorphic probes for whole genome coverage. This array provides an average intergenic probe density of one probe per 880 bases and an overall (gene and non-gene backbone) probe density of one probe every 1,148 bases.

Test Analysis

We analyze results using the Affymetrix Chromosome Analysis Suite 3.0 software. The analysis of the data is based on the most recent human genome build (hg19). All reported base pair coordinates are estimated. Deletions larger than 200 kb and duplications larger than 400 kb will generally be reported.

We report smaller copy number (CN) changes if they are considered clinically significant based on genomic information available at the time the report is issued. Benign CN variants will not be reported but will be kept on file in the laboratory. We report CN changes resulting in carrier status for autosomal recessive disorders if a concern for a specific disorder is communicated to the laboratory. 

We confirm CN changes using fluorescence in situ hybridization (FISH) or other appropriate methodologies concurrently when parental analysis is recommended. Long, continuous stretches of homology (LCSH), which can result from uniparental disomy (UPD) or common descent, can also be detected using the CytoScan HD array. Reported regions of LCSH will not be confirmed, but recommendations for further molecular testing may be made to confirm UPD or to identify recessive alleles possibly associated with the patient’s condition.


This test does not detect balanced chromosome rearrangements such as Robertsonian or other reciprocal translocations, inversions, or balanced insertions. It will not detect imbalances of regions not represented on the array, or all types and instances of uniparental disomy. This test is not designed to detect mosaicism at low levels.

Normal findings do not rule out the diagnosis of any disorder, since some genetic abnormalities may be undetectable with this assay. Specifically, this test does not detect point mutations, small deletions, or insertions below the resolution of this assay or other types of mutations, such as epigenetic changes.

Reporting Results

The results of this test may be of unclear clinical significance. In such cases, additional family studies may be necessary to interpret the results. Copy number variations (CNVs) detected by this platform may not be investigated or reported if they are devoid of relevant gene content, reported as common findings in the general population based on available database searches, or are gains smaller than 400 kb or losses smaller than 200 kb. It is appropriate to refer individuals and families to a clinical geneticist or counselor to discuss results of this test.