Genetics and Genomics Diagnostic Laboratory
Cytogenetics Laboratory | Frequently Asked Questions

Frequently Asked Questions about Single-Nucleotide Polymorphism (SNP) Microarray Testing

The Cytogenetics Laboratory team at Cincinnati Children’s Hospital Medical Center provides answers to frequent questions about single-nucleotide polymorphism (SNP) microarray testing.

This testing is an advance in cytogenetic technology that allows us to detect cytogenetic imbalances that are smaller than what can be detected through routine chromosome analysis. This test will be an invaluable tool for diagnosis in patients with a variety of indications when a chromosomal imbalance is suspected, but cannot be detected through traditional chromosome analysis.

Cincinnati Children’s Cytogenetics Laboratory offers testing that will detect the loss (deletion) or gain (duplication) of chromosomal regions.

Microarray SNP (MA-SNP) testing uses BeadChip technology to examine more than 1 million separate chromosomal regions. We use the Infinium Assay with the Illumina HD HumanOmni1-quad BeadChip platform in our SNP (single- nucleotide polymorphism) based platform. This array is used to detect chromosomal imbalances throughout the genome. The resolution of this array can detect imbalances that are as small as 80-100 Kb with gaps in coverage of 1 megabase or less. This array can detect imbalances that may not be well-described. It may also be useful to further define breakpoints in imbalances that are already known.

Patients with chromosome imbalances may not have classic presentations, so with other technologies it may be difficult to decide which specific test to do. Now all of these regions can be examined with one test. Balanced or mosaic chromosome changes may not be identified with this technology. Traditional chromosome analysis is recommended before proceeding with pediatric cytogenetic microarray testing.

Our analysis includes use of DNA microarray technology to detect possible imbalances in more than 150 regions of common microdeletion / microduplication syndromes, all subtelomeric regions, the pseudoautosomal regions and across the genome. Microarray is completed using the the Infinium Assay with Illumina HumanOmni1-quad DNA Analysis BeadChip platform. This SNP array includes DNA from more than 1 million probes (copy number or SNP) covering all 24 chromosomes.

Using Illumina GenomeStudio analytical software, differences in copy number of different DNA clones can be detected. Imbalances detected may be confirmed by FISH analysis.

Studies have shown that approximately 10 percent of children with unexplained intellectual / developmental disabilities and dysmorphic features will have abnormalities detected through cytogenetic microarray testing. Microarray testing is indicated in any patient with a suspected chromosome imbalance. This includes patients with the following or combination of the following:

  • Developmental delay
  • Intellectual / Cognitive delay
  • Dysmorphic features
  • Congenital anomalies or malformations

If chromosome analysis is normal, we recommend cytogenetic microarray analysis as the next step unless a specific genetic condition is suspected. This is also the recommendation supported by the American College of Medical Genetics for evaluation of unexplained intellectual / developmental delay.

Cytogenetic microarray testing is one of many superior clinical tests offered within the Genetics and Genomics Diagnostic Laboratory Cytogenetics Laboratory. This test was designed with ordering clinicians in mind. Our goal is to offer the highest quality testing while offering clear results and clinical guidance for the physicians and other clinicians who use our services. Our comprehensive microarray testing includes:

  • Microarray SNP allowing for some of the most comprehensive array testing currently clinically available
  • Superior quality testing performed by experienced cytotechnologists
  • Expert result interpretation provided by board-certified cytogeneticists
  • Preliminary results available in one to two weeks if requested; final results in 14-21 days (prenatal) or 30 days (pediatric)
  • Clinically useful results reports designed by geneticists and genetic counselors with 50 years of combined clinical genetics experience
  • A team of board-certified and experienced cytogeneticists and genetic counselors available to assist you
The vast majority of known microdeletion / duplication syndromes will be detected using microarray. Subtelomere imbalances as well as imbalances in the pseudoautosomal regions also will be detected.  The SNP array interrogates more than 1 million probes over the genome to look for imbalances. This will allow for diagnosis of chromosomal imbalances not previously well-described.

This testing allows us to look at more than 150 specific microdeletion / duplication syndrome regions, subtelomeric regions and locations throughout the genome at one time. Early studies suggest 8 percent to 10 percent of patients with normal chromosome results may have an abnormality that can be detected with microarray testing. This is higher than the detection rate found with subtelomere analysis following chromosome testing. Microarray testing will allow for diagnosis of these known disorders in fetuses, children and adults with less obvious features of these conditions.

SNP microarray testing may enable the diagnosis of chromosomal imbalances that have been previously described in children and adults with your patient’s features. This may allow physicians to anticipate medical needs of those patients and direct their care more appropriately once a diagnosis has been made.

Balanced chromosomal rearrangements and mosaic chromosomal imbalances may cause developmental disabilities and dysmorphic features or congenital abnormalities in patients. These changes often cannot be detected using microarray. For this reason, it is recommended that a physician order chromosome analysis prior to ordering microarray testing. At Cincinnati Children’s, you can order both tests at the same time, and we will start microarray testing if chromosome analysis is normal (reflex testing as listed on requisition).

Genetic conditions may be caused not only by DNA imbalances, but also by point mutations or other genetic changes. If a specific genetic diagnosis is suspected, contact the laboratory for additional testing that may be recommended. Microarray technology may identify copy number variants or polymorphisms that are common in the general population, and these may not be associated with your patient’s features. Testing of biological parents may be requested to aid with clinical interpretation of results.

Preliminary results are available by request and may be phoned to the ordering physician in approximately one to two weeks. Call 513-636-4474.

Final written results and interpretation of any regions of imbalance that may have clinical significance will be sent to the ordering physician in 14-21 days for prenatal cases and within 30 days for pediatric patients.

We have provided links to academic papers if you would like more information on microarray testing in general.