Prenatal single gene testing

Also known as: Fulgent genetics prenatal test, Beacon prenatal test; Prenatal diagnostic test for known familial mutation(s)


Test category:

Reproductive - Fetal diagnosis

Use of test


Prenatal testing can be carried out to detect mutation(s) in a specific gene in the fetus when one or both parents are known to be carriers of a pathogenic variant (mutation). The parental carrier status may have been identified from earlier genetic studies such as reproductive carrier screening or previous testing with the family. Testing is carried out on DNA extracted from either a chorionic villus sample or an amniocentesis sample. Non-invasive single gene testing is not currently available.

In addition to testing for the specific familial single gene mutation(s), testing for chromosomal abnormalities can optionally be carried out on the same sample, by FISH analysis for aneuploidy of chromosomes 13, 18, 21 X or Y and microarray analysis for deletions and duplications in all chromosomes. 


Prenatal testing is generally restricted to clinically severe, single gene disorders.  Where one or both parents are known to carry pathogenic variants in a specific gene, presence or absence of the known variants in the prenatal sample provides specific diagnostic and prognostic information.

Testing for chromosomal aneuploidy, deletions and duplications across the genome by microarray can also provide diagnostic and prognostic information. Abnormalities detected by these methods can be inherited, or may arise de novo. Further family studies may clarify the recurrence risk in relatives.

Microarrays can also detect deletions and duplications that are of unknown clinical significance or which have variable clinical outcomes ('susceptibility variants'). Rarely, deletions or duplications which are associated with a clinically significant disorder unrelated to the presentation of the patient may be detected. The report will provide advice regarding the interpretation of such findings. Note that the absence of a pathogenic abnormality on microarray analysis does not necessarily exclude the possibility of any genetic condition in the fetus, as microarrays have a relatively limited resolution.

Ethical considerations:

This is an assay for mutations that may be heritable or de novo. It may raise issues of ethics or consent that are different from most other investigations ordered in the routine care of a patient. Responsibility for providing pre-test counselling and obtaining informed consent for this test rests with the practitioner requesting or performing the CVS or amniocentesis. Use of a specific request form is mandated to facilitate rapid processing and provide consent for sending an identified sample overseas.

Consent form:

Not applicable.


If the parental mutation/s were identified by the Beacon expanded carrier screen, the sample is sent for testing to Fulgent Genetics in California. Fulgent Genetics is a CLIA-accredited laboratory. They will test for previously identified parental pathogenic variants using sequencing methodology.

If the parental mutation/s were identified using a different test, we will contact the referring doctor to discuss the preferred laboratory for analysis.

For microarray testing, the relative amounts of genetic material from hundreds of thousands of small regions from all chromosomes are measured. Deviations from the expected values can identify deletions and duplications. Sonic Genetics uses a single nucleotide polymorphism (SNP) microarray, which provides additional genotype information compared with CGH microarray. SNP microarrays can identify large regions of homozygosity, which may be useful in detecting uniparental disomy or an increased likelihood of a recessive disorder.

Requesting the test


This test is usually requested by an obstetrician or clinical geneticist.

Request form:

Download the prenatal single gene prenatal single gene request form

Sample required:

Chorionic villus or amniotic fluid sample is required. An invasive procedure by an obstetrician is necessary to obtain this. A separate EDTA blood sample is also required from the mother, so that maternal cell contamination of the prenatal sample can be excluded.

To help ensure the quality of the test, a genetic test should be done with a dedicated sample whenever possible i.e. a sample collected specifically for that test rather than a sample that is used for multiple tests.

We recommend that the patient or another adult check the labelling of request forms and sample containers.

Special instructions:

Please include the results of the parental single gene mutation test on each parent with the request, to ensure that the correct mutation(s) are tested in the fetus.

Turnaround time:

Four to six weeks for familial mutation testing.

1-2 days for FISH, and 15 days for microarray/karyotype.


The cost for prenatal single gene testing is $595 when the familial mutations have been identified as part of the Beacon expanded carrier screen. Microarray analysis can be provided on request at no additional charge (subject to the Medicare requirements being met). Rapid FISH analysis for common aneuploidies is available for an additional fee of $100.

If the familial mutations have not been identified as part of the Beacon carrier screen, prenatal single gene testing may or may not be possible. In addition, the test fee will be higher, and may vary depending on the particular gene. Please contact the laboratory on 07 3377 8727 prior to invasive sample collection or referral to confirm that appropriate testing is available, and the test fee.   

Microarray testing has a Medicare rebate which, subject to the Medicare requirements being met, may cover all or part of the cost.


The Medicare details for microarray, including descriptor and schedule fee, are listed under MBS item 73287.

Click here for our billing policy.