In our previous article, we outlined the difference between chromosomal abnormalities and subtle genetic variants. While there is a wide variety of causes for these conditions, not all genetic tests are the same, and there is also a wide variety of tests that can estimate or confirm genetic and chromosomal risks.

An important distinction to be made in deciding between tests is the reliability of the result obtained. There are two important categories here: screening tests and diagnostic tests. 

Screening tests 

By definition, a screening test aims to estimate the likelihood of one or more health conditions. The determining factors of a screening test are the detection rate, which is intended to be as high as possible, and the probability of a false-positive result (i.e., results that will appear to be at high risk even though the disease is not present), which is intended to be as low as possible. 

In the context of prenatal screening for chromosomal abnormalities, the two main technologies available are: biochemical screening (by serum markers) with ultrasound measurement of the nuchal translucency if available, and non-invasive prenatal screening by cell-free DNA (generally referred to as non-invasive prenatal screening or testing). 

Prenatal biochemical or serum screening

This is the government’s screening test that is universally available to the general population of pregnant women in Quebec. Several markers made by the placenta are analysed to determine a risk, usually only for trisomies 21 and 18. The test covered by the Régie de l’assurance maladie du Québec involves two blood draws in the first and second trimester. There are options available in private clinics that can give a result with a single blood draw in the first trimester, combined with ultrasound measurement of the nuchal translucency*, offering a higher detection rate than the public screening test while ensuring a faster result. 

Depending on the risk assessed, additional tests such as non-invasive prenatal screening or prenatal diagnosis may be recommended. 

*Nuchal translucency measurement is sometimes also available in the public system, but this is not the case for all healthcare facilities currently. 

Non-invasive prenatal screening (NIPS) or Non-invasive prenatal testing (NIPT)

This is an analysis of DNA fragments from the placenta that are present in maternal blood to estimate the risk of a fetal chromosomal abnormality. Its detection rate is higher than biochemical or serum screening, making it the screening test with the highest detection rate for chromosomal abnormalities. 

A low-risk result, or no aneuploidy detected, indicates that the baby is unlikely to have one of the conditions targeted by the screening. A high-risk result indicates that there is a risk that the baby may have one of the conditions targeted by the test. An inconclusive result indicates that the analysis could not be completed. In this case, repeat analysis may be offered or genetic counselling recommended, depending on the situation. 

Although this result is very precise, a result indicating a high risk is less reliable for a patient without risk factors than for a patient who does have risk factors for having a child with a trisomy (e.g., advanced maternal age). 

Attention: A high-risk result is not a 100% confirmed diagnosis, and no decisions should be made for the pregnancy without a reliable diagnostic test. 

Invasive Diagnostic Tests  

As opposed to screening, a diagnostic test is a medical test that aims to confirm or rule out a possible diagnosis with certainty. 

In the prenatal setting, invasive diagnostic tests are available for any patient whose pregnancy has been identified as being at risk for a genetic or chromosomal condition. One of the most common reasons for these tests is the presence of a high risk at screening for a common chromosomal abnormality (trisomy 21, 18, 13 or sex chromosomes), but prenatal diagnosis is also indicated in the case of a risk of a genetic or chromosomal condition that could be inherited from the biological parents in connection with a medical or obstetric history, and/or following the identification of specific ultrasound signs. Depending on the reason for the diagnostic testing, different targeted tests may be performed on the sample. 

There are two main invasive procedures for prenatal diagnosis: chorionic villus sampling and amniocentesis. 

Chorionic villus sampling (CVS)

Chorionic villus sampling is only available in some hospital centers and can only be performed over a short period of time, generally between the 10th and 14th week, depending on the center. Always performed under ultrasound guidance, this procedure removes a small sample of placental tissue intravaginally or intra-abdominally depending on the location of the placenta. This sample allows for earlier analysis than amniocentesis. In 1-2% of cases, the result is inconclusive due to maternal cell contamination. This means that the sample could represent DNA from the mother and not that of the placenta. 

Amniocentesis

Amniocentesis is generally available from 15 weeks of pregnancy and consists of removing a sample of amniotic fluid through the abdomen, under ultrasound guidance. This fluid contains many cells from the fetus, including from the skin and urinary system, and will allow direct analysis of fetal DNA.  

In either case, chorionic villus sampling and amniocentesis techniques are invasive and are therefore associated with risks, that can include miscarriage or premature delivery, depending on gestational age. It is therefore important to access genetic counselling to help with the decision of whether to perform one of these procedures, based on the assessment of the estimated risks for the current pregnancy. These invasive procedures are generally available when the risk of identifying a genetic or chromosomal abnormality is greater than or equal to the risk of fetal loss associated with the procedure. 

Genetic testing following invasive sampling

Chorionic villus sampling and amniocentesis are just procedures to obtain a DNA sample. In the same way as with a blood or saliva sample, once the sample has been obtained, many different tests can be done. The specific type of test will depend on what kind of risk needs to be assessed. 

• Karyotype analysis evaluates the copy number and structure of the chromosomes. It is non-targeted and will look at all of the chromosomes. It is a fairly standard test that can be prescribed by any doctor, and is indicated in many clinical settings (e.g., suspicion of a chromosomal translocation, risk of trisomy in a pregnancy, recurrent miscarriages, diagnosis of developmental delay, early ovarian insufficiency, azoospermia, etc.). Here, only whole chromosomes and large pieces of missing or duplicated chromosomes are visible. Prenatal samples are usually first assessed with a faster test called FISH or QF-PCR to assess the chromosomes that are more likely to be abnormal (13, 18, 21, X and Y).
• CGH microarray tests are also non-targeted and assess all chromosomes for additional small pieces of chromosomal material (microduplications) or missing material (microdeletions). It is a more in-depth analysis that is mostly prescribed by geneticists in specific contexts (e.g., suspicion of a prenatal or neonatal syndromic genetic condition, identification of a chromosomal rearrangement that could have led to a loss of chromosomal material at the break points, etc.). 
• Sequencing tests are precise molecular techniques that assess for the presence of subtle genetic changes (or “misspellings” in the DNA). When the reason for the test is to rule out a specific genetic variant or health condition, sequencing may only focus on a single gene. In some situations, panels of dozens or hundreds of genes will be indicated, for example when we are trying to identify the cause of a syndromic genetic condition visible on ultrasound (usually following a normal microarray result) and we want to assess multiple possible diagnoses. 

Beyond the prenatal context, these sequencing panels are used when several genes are involved in the same health condition in a child or adult (e.g., hereditary breast cancer predisposition panel, cardiac genetic disease panel, neurodevelopmental panel). Another example of a panel involving several hundred genes is the expanded carrier genetic test, which aims to assess the preconception risk of passing on a genetic condition to one’s children. 

 If we go back to the specific context of an ongoing pregnancy, regardless of the initial reason for this procedure, the first test performed usually includes the common viable aneuploidies (trisomies 21, 18, 13 and sex chromosomes). If the only known risk is for frequent trisomies, no further analysis will be performed. Depending on the situation, if there are particular ultrasound findings or a specific condition to rule out in relation to a medical or family history, microarray analysis and/or targeted sequencing tests or molecular panels of several genes could be performed subsequently. 

The field of medical genetics is complex! If you have any doubts about your eligibility for specific genetic testing, don’t hesitate to talk to your doctor and ask to be referred for genetic counselling.