Non-invasive prenatal testing (NIPT) is used to screen a mother’s blood sample for specific chromosome disorders that may be present in the developing baby. In 1–2% of women, the NIPT result is unable to provide an assessment about one or more of the disorders being screened, or cannot provide an assessment of fetal sex. This is usually due to the complexity of pregnancy rather than a technical failure of the test. This outcome may be frustrating for the woman and her doctor. So why do some NIPT tests not provide a result?
How NIPT works
The mother’s blood contains small fragments of DNA from both the mother and the placenta. The placenta is derived from the same fertilised egg as the developing baby, and usually has the same genetic makeup as the baby. The proportion of these DNA fragments that came from a specific chromosome is very stable throughout pregnancy and in different women.
If there is an excess of placental DNA fragments from one chromosome, the overall proportion of fragments from that chromosome will differ from what is expected.
If there is sufficient fetal DNA in the sample, NIPT can either confirm that the proportion of fragments is as expected (low probability of disorder being present) or detect a change in proportion (high probability for that disorder).
When testing the blood sample from a pregnant woman, NIPT depends on three inter-related factors:
The proportions of DNA fragments from different chromosomes must be the same as are found in the general population. A woman or the placenta may have an uncommon variation in the amount of DNA in a chromosome that is, of itself, harmless but it alters the relative proportions that are measured for other chromosomes. This may make it impossible to reliably determine whether the proportion for a particular chromosome is within normal limits.
There must be sufficient DNA fragments from the placenta in the maternal blood. If there is very little placental DNA in the mother’s blood, any change in the proportion of fragments from the placenta or baby will be masked by the much larger contribution of DNA fragments from the mother. This makes it impossible to reliably detect any chromosome disorder in the baby.
There must be sufficient DNA fragments that can be assessed by the test to be confident of the result. Our NIPT methods count millions of DNA fragments in every sample so that we have very precise estimates of the proportions of fragments from different chromosomes. The number of fragments that need to be counted will vary in different blood samples. In either of the two situations above, we would need to count even more fragments to achieve a reliable result. This requirement is complicated by some chromosomes (such as the X and Y chromosomes) being less informative than others, that is, each DNA fragment is harder to assign to a given chromosome.
If NIPT cannot be reported at all
A possible reason for this is that there are too few DNA fragments from the placenta compared with the maternal fragments, that is, low fetal fraction. The fetal fraction can vary over time. It is more likely to be low in women with increased body weight, and may be more likely with infection, inflammation, certain medications, such as clexane, or exercise.
This outcome can also be due to variations in proportions of DNA from different chromosomes in the mother or placenta, or from a demised twin.
If the problem is primarily low fetal fraction, it may be worth repeating the NIPT (at no additional cost). Approximately half of such recollections will yield a result. Please note that recollection is not routinely recommended; the laboratory will advise if recollection is recommended.
If NIPT cannot provide an assessment after one collection (or two, if recommended by the laboratory), it is not worth repeating the NIPT. A decision about other tests (maternal serum screening, detailed ultrasound, CVS or amniocentesis) should be based on the doctor’s assessment of all risk factors identified, and may require specialist consultation. The risk of trisomy may be increased in patients with persistently low fetal fraction.
If NIPT reports a result for trisomies, but not for fetal sex
The Y chromosome (indicating a male fetus) is smaller than the other chromosomes. Determining the presence or absence of the Y chromosome can be compromised by factors which do not limit reporting an assessment of other chromosomes. These factors include the fetal fraction being at the lower end of the acceptable range for trisomy testing, benign variation in the structure of the Y chromosome, and the quality of the DNA in the sample.
It is not worth repeating the NIPT as it is unlikely that the repeat test will provide a clear result for fetal sex. A decision about using fetal ultrasound or invasive genetic testing to document fetal sex should be based on the doctor’s assessment of need and any risk factors identified.
If NIPT reports a result for trisomies, but not for sex chromosome aneuploidies
Assessment of the numbers of X and Y chromosomes raises specific challenges.
The Y chromosome is the smallest chromosome. There are technical challenges in determining the number of Y chromosomes.
Most of the DNA fragments in maternal plasma come from the mother (two X chromosomes), and the test must count the number of X chromosomes (one, two or three) in the smaller number of fragments from the placenta.
Benign variation in the structure of the X chromosome is relatively common, complicating the reliable assessment of X chromosome number in the placenta.
The mother or placenta may have some cells with an abnormal number of X chromosomes. This is relatively common and may be harmless, however, it complicates reliable assessment of X chromosome number.
It is not worth repeating the NIPT as it is unlikely that the repeat test will provide a clear result for sex chromosome aneuploidy. A decision about using fetal ultrasound or invasive genetic testing to assess the fetal sex chromosomes should be based on the doctor’s assessment of need and any risk factors identified.
The primary purpose of NIPT is to screen for the common trisomies of chromosomes 21 (Down syndrome), 18 (Edwards syndrome), and 13 (Patau syndrome). If NIPT cannot provide an assessment for these disorders after one collection (or two, if recommended by the laboratory), a full refund will be offered.
The assessments of fetal sex and of sex chromosome aneuploidies are optional tests that are provided at no additional cost. There is no refund available if an assessment of trisomies is reported, but an assessment of fetal sex or sex chromosomes was not.