A chromosome microarray (CMA or molecular karyotype) is a powerful tool used to look at very small changes in our genetic information that may affect health and/or normal development.

A microarray is the recommended first line genetic test for developmental delay (DD), intellectual disability (ID) and autism spectrum disorders (ASD)*.

CMA however, does not identify fragile X syndrome (FXS), a common cause of intellectual disability. Therefore, a DNA test for FXS must be ordered alongside a CMA. A Medicare rebate is available for both tests.

  • CMA and FXS testing at VCGS can be performed using saliva instead of blood
  • Our testing is bulk billed
* Miller, D.T., et al, Consensus statement: Chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010; 86: 749–764

Order microarray and fragile X testing online
These tests can be ordered through our online test request system.

What is this test?

A chromosome microarray in the paediatric setting is used to identify very small changes in our genetic information (DNA) that may be the cause of developmental or other health concerns in children. It is a more powerful test than a conventional chromosome analysis (karyotype).

These small changes in DNA are known as copy number variants (CNVs). A CNV is a small piece of extra or missing DNA (duplications and deletions). Everyone has CNVs in their DNA and most do not affect health. However, some CNVs are known or highly suspected to affect health and development.

A microarray detects the likely cause of a range of developmental concerns in about 15% of referrals.*

* Battaglia et al., 2013 Confirmation of chromosomal microarray as a first-tier clinical diagnostic test for individuals with developmental delay, intellectual disability, autism spectrum disorders and dysmorphic features. Eur J Paediatr Neurol. 2013 Nov;17(6):589-99)
What conditions does this test look for?

A microarray replaces most tests looking for CNVs (e.g. microdeletion and microduplication syndromes), but does not replace all other genetic investigations. Tests with complex genetics, like fragile X syndrome, need to be requested and performed separately.

When a CNV is identified in a child, parental testing is often requested as a next step. This can help to determine whether a CNV has been inherited, and in some cases, can assist the lab in interpreting the possible significance of the CNV.

If you aren’t sure if microarray is the most appropriate test for your patient, or why parental testing has been requested, please contact our paediatric genetic counsellor.

P: 1300 118 247
E: [email protected]

Paediatric Microarray

Interphase Fluorescent in situ Hybridisation or FISH, is a technique use in the paediatric setting to provide rapid results for the detection of chromosomal trisomies like Down syndrome (trisomy 21). FISH may also be used for urgent microdeletion syndrome confirmation and to diagnose certain classes of paediatric cancers. Interphase FISH is a useful technique because it uses uncultured cells, meaning it can provide rapid test turn around times (usually within 24-48 hours).

View Test & Specification requirements

A chromosome microarray is a powerful tool used to look at sub microscopic changes in our genetic information that may impact health or development. Microarray is considered the gold standard test for the investigation of intellectual disability and developmental and behavioural concerns such as autism spectrum disorders and congenital malformations.

View Test & Specification requirements

The investigation of microdeletion and microduplication syndromes is now performed by microarray analysis. Microarray provides a superior investigation than FISH testing as it detect a wider range of genetic changes that may cause each syndrome. If an urgent investigation is required, FISH can be performed in 24-48 hours - please contact us to arrange testing.

View Test & Specification requirements
How do I arrange a test?

Microarray testing is typically arranged through a paediatrician, a clinical genetics service or in some cases, a GP. A completed test request form is required. Testing can be performed on blood or saliva. You can also arrange for a saliva kit to be sent directly to your patient’s home address. They can return it to VCGS free of charge.

Frequently asked questions

How much does a paediatric microarray cost?

There is a Medicare rebate for paediatric microarray testing, so there are no out of pocket costs. If a Medicare number is supplied, testing will be bulk billed.

For institutional charging refer to the microarray test and specimen requirements.

How will I get my results?

Microarray testing typically takes between 2-3 weeks. If testing for fragile X syndrome is also requested, the total time can be 2-4 weeks.

Results will be sent to your referring doctor. They will discuss any significant results with you and may refer you to a genetic counsellor if appropriate.

What do my results mean?

Copy number variants identified by microarray testing are reported a number of ways.

  • Pathogenic variants – the variant found is associated with a known medical condition. This information can help support clinical management of patients.
  • Variants of uncertain significance – the health impact of these variants is uncertain. There is some evidence that links the variant with a medical condition, but these variants can show incomplete penetrance. This means that not every individual that has this type of variant will be have the same health concerns. Some individual may have serious health impacts whilst others may be mildy or apprently unaffected. Testing of parents or other family members is usually recommended.
  • Variants of unknown significance – the health impact of these variants is unknown as there is very little information in the medical literature. Testing of parents or other family members may help to further investigate these variants.
  • Incidental findings – these variants can be associated with medical conditions that are unrelated to the conditions being investigated. They are infrequent, but mean that families receive unexpected information. Incidental findings can require follow-up testing and genetic counselling.
  • Long continuous stretches of homozygosity (LCSH) – in most cases a finding of LCSH will not be relevant to the patients condition, however occasionally can be associated with a specific group of genetic conditions called imprinting disorders (e.g. Prader-Willi and Angelman syndrome). Specific LCSH analysis can be useful when a recessive genetic condition is suspected.
  • Benign variants – these are frequently found in individuals without health concerns. Benign variants are not reported.

My child had microarray testing and now I need to have the test. Why?

If a copy number variant is detected in your child, testing of parents is useful. This can help determine the significance of the variant found in your child and determine your risk of having another child with the same or related genetic condition.

Because the genetics of some conditions is complex, a CNV detected in one individual may have a significant affect on their development, whilst a parent with the same CNV may have no obvious health concerns. This is known as incomplete penetrance. A discussion with your doctor is required to help explain the relevance of any copy number variant that has been detected.

What happens to my genetic information?

Microarray testing generates a large amount of genetic information. Access to and storage of genetic information is strictly governed by national laboratory and health privacy guidelines, to which VCGS adheres.