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

In the paediatric setting, a chromosome microarray (or molecular karyotype) is the recommended first line genetic test for developmental delay (DD), intelectual 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 at VCGS can be performed using saliva instead of blood
  • We offer combined CMA/FXS testing
  • Our testing is bulk billed
* Miller, D.T., et al, Concensus 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
What is this test?

A chromosome microarray in the paediatric setting is used to identify sub-microscopic genetic changes in DNA that may be the cause of developmental or other health problems in children.

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 is a more powerful test then conventional chromosome analysis as it is better able to detect very small CNVs.

What conditions does this test look for?

A paediatric microarray is specifically looking for CNVs that affect health. A microarray is an appropriate test for the investigation of genetic causes of intellectual disability, developmental and behavioural conditions such as autism spectrum disorders, congenital malformations and for some familial genetic conditions. A microarray detects the likely cause of developmental problems in about 15% of referrals.

A microarray replaces most tests looking at microdeletion and microduplication syndromes (eg Di-George syndrome), but does not replace all other genetic investigations. Tests with complex genetics, like fragile X syndrome, need to be requested and performed separately. For specific information on microarray testing, please contact the laboratory.

Parental microarray testing is often required and may be used to help determine the significance of some CNVs, where the clinical significance is yet to be fully determined.

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) and to diagnose certain classes of paediatric cancers.

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 7-10 days.

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

Microarray testing is arranged through a paediatrician, genetic counsellor or in some cases, a GP. A completed test request form is required.

Microarray can be performed on either a blood or a saliva sample. We supply saliva collection kits at no charge (including reply paid packaging). We can even send these kits directly to your patient's home address (complete a saliva kit request form in addition to the test request form).

VCGS supplies saliva collection kits at no charge and includes reply paid packaging.

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.

How can I speak to someone about my child’s microarray result?

Your doctor will discuss your microarray result with you. If you wish to discuss this further then you can see one of our specialist genetic doctors or counsellors. VCGS conducts clinics in Victoria, Tasmania and the Northern Territory and your doctor can arrange a referral to be seen in one of these clinics.

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.

How much experience does VCGS have with microarrays?

The Victorian Clinical Genetics Services (VCGS) was the first service in Australia to offer diagnostic microarray testing. Since 2007 we have performed over 60,000 microarray tests making VCGS the most experienced service in Australasia. All microarray analysis performed at VCGS are fully supported by a team of clinical geneticists and genetic counsellors that provide expert interpretation and support services.