cfDNA test GENNET

Screening of cell-free foetal DNA (cfDNA) from the blood of a pregnant woman to detect aneuploidy of sex and non-sex chromosomes of the aborted foetus and its gender. From week 10 of the pregnancy.

The cfDNA Test GENNET, a non-invasive prenatal test (NIPT), detects the presence of deoxyribonucleic acid (cfDNA) fragments freely circulating in maternal plasma according to their chromosome affiliation. Deviations from the expected representation of fragments, which are a mixture of DNA originating from placental cells and maternal cells, increase the risk of changing the number (aneuploidy) of a given chromosome or its part (structural aberrations) in the foetus. The cfDNA Test GENNET uses VeriSeq NIPT v2 Solution CE-IVD certified automated technology, protocol and data analysis from Illumina. Two types of risk assessment (screening) for aneuploidy can be selected – basic and whole-genome. Basic screening is focused on the risks of the most common aneuploidy: chromosome 21 multiplication (trisomy) causing Down syndrome, chromosome 18 multiplication (Edwards syndrome), chromosome 13 multiplication (Patau syndrome) and sex chromosome X and Y aneuploidy causing Turner syndrome, Klinefelter syndrome, Jacobs syndrome and Tripple X syndrome. Genome-wide screening of uncommon (secondary) findings detects aneuploidy of all chromosomes and their partial multiplication (duplication) and loss (deletion) of at least 7Mb. For both types of screening, it is possible to choose whether to test the sex of the foetus. The cfDNA Test GENNET detects more than 99% of chromosome 21, 18 and 13 aneuploidy with a false positive rate of less than 1% (this is when a positive NIPT test result is not confirmed by direct foetal examination by amniocentesis). The sensitivity of the test is lower and the false positive is higher for X and Y sex chromosome aneuploidy and secondary findings. These chromosomal aberrations are more often limited to the placenta (placental mosaic) or are of maternal origin. The sex of the foetus (if required) is determined with an accuracy of more than 99%. 

Test limitations: 

cfDNA Test GENNET is a genetic screening test that has limitations. It is one of the components of the prenatal screening programme and is currently not suitable as a first-line screening test or in ultrasound findings. The result of the cfDNA Test should always be interpreted individually, taking into account the results of previous examinations and the opinion of the pregnant woman. Definitive evidence of chromosomal aberration in the foetus can be obtained by only targeted (diagnostic) examination of foetal tissues, most often by amniotic fluid sampling (amniocentesis). We always recommend detailed ultrasound examination in week 20–22 of the pregnancy. The results of the genetic test should be consulted with a clinician or treating physician. The accuracy of the test depends on the proportion of cfDNA that originates from the placenta (the so-called foetal fraction) and its quality. A low foetal fraction can be expected in early pregnancy, in the plasma of mothers who are overweight or who are being treated with anticoagulants, and may persist throughout pregnancy. With low foetal fraction or reduced quality of cfDNA, the result cannot be reported or is inconclusive. The results of the cfDNA Test GENNET – especially secondary findings – can also be affected by a number of maternal factors: e.g. blood transfusion, organ transplant, stem cell therapy, surgery, immunotherapy, cancer, chronic inflammation or congenital chromosomal abnormalities. The results of the cfDNA Test GENNET in twins are sufficiently sensitive and have a low false positive rate. However, it is not possible to report the test result in up to 4% of twin pregnancies. In the case of vanishing twin syndrome, the result can be false positive in up to 5% of cases. When examining the sex of twins, only the presence or absence of the Y chromosome can be detected. If the Y chromosome is present, it is not possible to determine whether it is a sister and brother or two brothers. Although the cfDNA Test GENNET methodology is based on genome-wide analysis, certain regions of the genome are excluded from the analysis. They are listed in the VeriSeq NIPT Solution v2 Excluded Regions File on the manufacturer’s website (illumina.com). 

The cfDNA Test GENNET does not detect partial aneuploidy of less than 7Mb. 

The test has not been validated for: 

•  use in triple and multiple pregnancies; 
• detection of polyploidy (multiplication of complete sets of chromosomes, not just one chromosome); 
• detection of balanced chromosomal rearrangements; 
• detection of sex chromosome aneuploidy other than: XO, XXX, XXY and XYY; 
• detection of uniparental disomy (the foetus inherited both chromosomes from one parent); 
• monogenic/polygenic disease of the foetus.  

cfDNA test is part of the screening programme of the GENNET Clinic – indication for testing is the risk of combined first trimester screening in the range of 1/100–1/500 for a foetus without ultrasound findings