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Genomics in general practice

Genetic tests and technologies

Prenatal testing


All pregnant women (ie regardless of age, ethnicity, family history) should be provided with information about prenatal screening tests for chromosomal conditions such as Down syndrome and for autosomal and X-linked conditions. Screening options should be discussed in the first trimester whenever possible. 

Prenatal screening tests should not be considered routine, but offered as a choice to women. GPs should support women and couples to make informed, independent decisions about the utility of prenatal testing and reproductive options. Women who receive a high-risk screening result should be offered information about diagnostic testing.

What do I need to know?

Prenatal vs carrier screening. Carrier screening involves testing of the biological parents to see if they are carriers of a genetic condition vs prenatal screening which involves testing the pregnant woman and/or baby to look for the presence of a genetic condition in the baby.

Pre-pregnancy and pregnancy counselling that are relevant to genetics should include:

  • Any known genetic conditions among close family members (refer to ‘Family history’).
  • History of intellectual disability (ID), multiple pregnancy loss, stillbirth, children with congenital abnormalities 
  • Consanguinity Consanguinity describes a relationship between two people who are related to each other because of a common ancestor. Consanguineous relationships occur in all population groups, but occur more frequently in certain cultures. The most common form of consanguineous relationships is between first cousins. Individuals who are blood relatives share a greater proportion of their genes than unrelated people, thus, these individuals potentially share pathogenic variants for the same autosomal recessive condition. When individuals are first cousins and there is no family history of a specific condition, or of other consanguineous relationships in previous generations, the risk of them having a child with a medical condition is approximately 5–6%, compared with 3–4% in the general population. This risk is higher in couples where there is a multi-generational tradition of first-cousin marriages, rendering couples closer in genetic relationship. (‘are you and your partner blood relatives? Eg cousins’).
  • Pre-pregnancy and pregnancy folic acid intake
  • Information about carrier screening for inherited conditions (ideally pre-conception but if not possible then early in first trimester).

All women should be provided information about prenatal screening for chromosomal conditions. These cannot be screened for as part of preconception screening.

While chromosomal conditions such as Down syndrome are more common in pregnancies of women who are older (the chance of the baby having such a condition tends to increase with maternal age) younger women can also have pregnancies with chromosomal conditions.

Prenatal screening information should include the following:

  • Presenting the various screening options and their timing
  • An explanation of the meaning of results
  • A discussion of the potential implications of receiving a positive screening result (ie the possibility of an invasive diagnostic procedure such as chorionic villus sampling (CVS) and amniocentesis, thinking about the possibility of having a child with special needs or pregnancy termination, the availability of preimplantation genetic diagnosis).

Other important considerations:

  • Screening tests can determine who is at increased risk of having a baby with a chromosomal or inherited condition. Women who choose to undertake screening tests should be informed that they will be offered invasive diagnostic testing if they receive a high-risk screening Individuals may choose not to proceed with diagnostic testing for a number of reasons (eg concern about risk of miscarriage, not wishing to know prior to the birth, termination of pregnancy is not an option).
  • There is no increased risk of miscarriage from screening tests.
  • Every screening test has a false positive rate: some women will receive an ‘increased risk’ result even though their baby is unaffected
  • ‘Low-risk’ results do not exclude Down syndrome or other conditions
  • A second trimester ultrasound may detect some physical problems, but it is not recommended as a screening test for Down Syndrome 
  • Use of the term ‘risk’ in relation to the probability of a diagnosis of Down syndrome (or other disability) should be avoided when discussing prenatal screening with patients because it implies a negative consequence, and can cause offence. The recommended terminology is ‘chance’ or ‘probability’.

Genetic testing

Combined first trimester screening

Combined first trimester screening (CFTS) adds different measures together to provide a risk estimate for Down syndrome (trisomy 21), Edwards syndrome (trisomy 18) and Patau syndrome (trisomy 13).

These measures are as follows:

  • Maternal blood to measure pregnancy-associated plasma protein A (PAPP-A) and free ß-subunit of human chorionic gonadotrophin (ß-hCG). Levels of these proteins vary, but tend to be different in women carrying fetuses with Down syndrome or trisomy Increased free ß-hCG with decreased PAPP-A is suggestive of Down syndrome, while decreased levels of both analytes is suggestive of trisomy 18.
  • A nuchal translucency (NT) screening ultrasound
  • Maternal age, weight and gestation age
  • In some cases the presence or absence of nasal bone on ultrasound is added to the algorithm.

Approximately 5% of CFTS tests give an increased risk result. This figure varies depending on maternal age. Women with an increased risk result should be offered a diagnostic test. The majority of increased risk results are not due to Down syndrome, and most of these babies will be healthy.

There is a partial Medicare Benefits Schedule (MBS) rebate for the blood test component of CFTS; however, there are out-of-pocket expenses for the ultrasound.

Second trimester maternal serum screening

Second trimester maternal serum screening uses a blood test in conjunction with maternal age and weight, and gestational age to calculate a risk estimate of the chance a pregnancy is affected by Down syndrome, trisomy 18 or neural tube defects (eg spina bifida).

CFTS and NIPT have largely replaced second trimester screening. Second trimester maternal serum screening is for women presenting late in pregnancy. The optimal time to have this test performed is between 15 and 17 weeks, but it can be performed until 20 weeks.

In some cases, there is no out-of-pocket cost for second trimester screening (ie public patient in a public hospital).

Non-invasive prenatal testing or screening

Non-invasive prenatal testing (NIPT; also called non-invasive prenatal screening [NIPS], cell-free DNA [cfDNA] testing) analyses cell-free fetal DNA found circulating in maternal blood. Testing is usually available from 10 weeks’ gestation. This test analyses the relative proportion of DNA fragments from different chromosomes. If the proportion of fragments from a specific chromosome is increased, then aneuploidy is suspected.

NIPT is the most accurate screening test available for detecting Down syndrome. Most available NIPT results will provide a risk estimate for trisomies 21, 18 and 13, and sex chromosome aneuploidies (eg monosomy X). Some also provide information about microdeletion syndromes, fetal sex and other autosomal aneuploidies.

While the accuracy of NIPT in identifying Down syndrome is very high, the accuracy is not as high for trisomy 13 or 18 or for sex chromosome aneuploidy. The accuracy of NIPT is also influenced by the age of the woman and prevalence of the particular condition. For example, the positive predictive value (PPV) will be lower in younger women in whom the prevalence of chromosome aneuploidies is lower.

NIPT does not screen for:

  • all chromosome aneuploidies
  • single-gene disorders
  • neural tube defects

High-risk results should be confirmed through diagnostic testing. False positive results are possible, and rates vary according to condition.

In some cases, NIPT can be performed as a second-tier screening test before progressing to chorionic villus sampling (CVS) or amniocentesis. Given the higher test sensitivity, a negative NIPT result can reduce the need for CVS or amniocentesis.

Currently, NIPT is not available through the MBS or covered by private health insurance.

Figure 1. Summary of prenatal tests


Screening tests



Diagnostic procedures*


Combined first trimester screening (CFTS)

Second trimester serum screening

Non-invasive prenatal testing (NIPT)**

Chorionic villus sampling (CVS); amniocentesis

Type of test

Blood test (maternal); ultrasound

Blood test (maternal)

Blood test (maternal)

Needle aspirate of

placenta or amniotic fluid


Nuchal translucency, pregnancy- associated plasma protein A (PAPP-A), ß-subunit of human chorionic gonadotrophin (ß-hCG)

Estriol, beta-HCG, alphafetoprotein, inhibin A

Plasma cell-free DNA

Fetal cells

Timing of test (weeks)

Blood and ultrasound 11-13 weeks

15-20 weeks

From 10 weeks

CVS 11-13 weeks Amniocentesis ≥15 weeks

Conditions detected

Trisomies 21, 18, 13; structural anomalies

Trisomies 21 and 18; neural tube defects

Trisomies 21, 18, 13; sex chromosome conditions* and other aneuploidies for some tests

Many chromosome and genetic conditions

Detection rate for trisomy 21





False positive rate for trisomy 21





Test failure rate





Risk to pregnancy




Small risk of miscarriage (≤1%)

*Though not highly accurate and can be confounded by underlying maternal and fetal factors.

** There are many different commercial tests available with varying characteristics (what is tested for, sensitivity, specificity and PPV), costs, etc.

†Diagnostic tests performed using fetal cells collected by diagnostic procedures include fluorescence in situ hybridisation (FISH), quantitative fluorescence polymerase chain reaction (QF-PCR), karyotype, and chromosome microarray (CMA).

Adapted from Murdoch Childrens Research Institute. Your choice – Prenatal screening tests in pregnancy. Melbourne: Murdoch Childrens Research Institute, 2017. 

When should I refer?

The following people should be offered referral to specialist services (genetics or obstetrics):

  • Couples who are known carriers of a genetic Such couples could access pre-implantation genetic testing Pre-implantation genetic testing is testing performed on embryos produced by IVF. Prenatal testing of successful pregnancies may be undertaken as pre-implantation genetic testing is less than 100% accurate. through in-vitro fertilisation (IVF) for future pregnancies.
  • Women with an increased probability of a pregnancy with a chromosomal condition
    • previous pregnancy with a chromosomal condition
    • positive screening test or diagnostic test
    • parent with chromosomal rearrangement (eg Balanced translocation A balanced translocation is a rearrangement of the chromosome with no apparent loss or gain of chromosomal material. Individuals with balanced translocations do not usually show any symptoms. ).
  • Women with confirmed abnormality from diagnostic testing

Further reading

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