History of NIPT throughout the world and in Slovakia:
|1997||discovery of free circulating fetal DNA,|
|1997||non-invasive fetal sex determination using the detection of Y-chromosome sequences,|
|1998||quantitative analysis of free fetal DNA in the maternal circulatory system,|
|1998||non-invasive fetal RhD status determination the,|
|1999||rapid elimination of free fetal DNA after birth demonstrated,|
|2000||non-invasive DNA testing focused on monogenic inherited congenital disorders (achondroplasia),|
|2008||pilot studies focusing on non-invasive fetal aneuploidy detection,|
|2009||first application and confirmation of the concept based on the potential of new generation sequencing (NGS) in detecting fetal trisomy 21,|
|2010||diversity of maternal and fetal DNA fragmentation characterized in detail,|
|2010||detailed fetal genome maps determined non-invasively,|
|2011||commercial NIPT available for the first time,|
|2012||complete fetal genome sequence obtained non-invasively,|
|2015||the first fetal DNA test based on maternal blood is introduced to Slovakia and used in clinical practice – TRISOMY test.|
|2017||TRISOMY test used more widely along with its the TRISOMY test + variant, which is designed to detect additional chromosome aberrations|
Our screening test is based on analyzing the whole genome sequence of free fetal DNA isolated from the peripheral blood of a pregnant woman. The data obtained by the sequenator analysis with low coverage is evaluated using a custom calculation algorithm and verified in accordance with the procedure published by Brianchi et al. (2012). *
* Bianchi DW et al. Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol. 2012 May; 119 (5):890 – 901.
A Unique Blood Sample Preparation Procedure
The TRISOMY test laboratory procedure includes a unique process that ensures an increased proportion of foetal DNA compared to the initial amount. This is achieved thanks to the physical difference between foetal DNA and maternal DNA. Using this unique procedure for processing TRISOMY test samples, the laboratory typically manages to obtain an average foetal DNA proportion of 16% (the average proportion of foetal DNA in the published studies ranges from 10 to 13%). More importantly, no set of samples processed using this special procedure has achieved a lower proportion of foetal DNA than 7.5%, which significantly reduces the risk of test failure caused by a low content of foetal DNA fraction in the examined sample.
Applying our preparation, analysis and evaluation method characteristics to samples obtained from the pregnant women with healthy foetuses and the pregnant women with chromosome 21 trisomy foetuses used within our validation study, it is statistically possible to estimate the occurrence of false positive and false negative results depending on the portion of foetal DNA in maternal blood. Based on existing information, we know that the proportion of foetal DNA in maternal blood varies from subject to subject and the occurrence of samples with a low foetal fraction (< 4%) has been detected in less than 5% of pregnant women (the average proportion of foetal DNA is about 14.5 %).***
Comprising 164 analyzed samples taken from pregnant women with a normal fetus and 39 pregnant women with detected trisomy 21, our validation study suggests that an average proportion of fetal DNA in the samples obtained from pregnant women whose fetus suffered trisomy 21 amounted to 16 % (the blue curve in Graph 1). If the proportion of fetal DNA in maternal circulation gives such values, the probability of obtaining a non-informative result is ~ 1:3 x 1013 and the probability of obtaining a false negative result (i.e. wrong) is lower than 1:9×1018.
The probability of obtaining a non-informative result in a sample with the lowest proportion of foetal DNA observed in our study (7.5 %; see the red curve) is ~ 1:15, and the probability of obtaining a false negative (i.e. wrong) result is less than 1:740.
The analysis of samples from pregnant women with healthy foetuses (blue curve) suggests that the probability of obtaining a non-informative result is ~ 1: 161 and the probability of obtaining a false negative (i.e. wrong) result is less than 1:30,000.
In order to minimise the risk of obtaining a false negative or a false positive result caused by naturally occurring pregnancies with a low foetal fraction, the results of our analysis are evaluated with regards to a special zone that defines non-informative results – the so-called “grey zone”. In Graph 2, this zone is illustrated by grey shading. If an analysed sample falls within this zone, it is necessary to analyse it again. In this connection, another blood sample must be taken 14 days after the previous sampling.
*** Hudecova I, Sahota D, Heung MM, Jin Y, Lee WS, Leung TY, Lo YM, Chiu RW.Maternal plasma fetal DNA fractions in pregnancies with low and high risks for fetal chromosomal aneuploidies.PLoS One. 2014 Feb 28;9(2):e88484. doi: 10.1371/journal.pone.0088484
Data Evaluation Based on a Custom Algorithm
Obtained using whole-genome free foetal DNA sequencing analysis, data corresponding to individual NIPTs is evaluated using complex mathematical models. NIPT data sets vary from laboratory to laboratory and also depending on the procedure used. The objective of the evaluation is to calculate what is called the Z-score (Graph 4).
Compared to the calculation methods used by our competitors, the advanced custom algorithm we use for TRISOMY test data evaluation allows us to achieve a higher average Z-score value with regard to the evaluated samples.
The higher median value of the Z-score in positive samples achieved using our advanced algorithm for TRISOMY test evaluation is automatically reflected in a more accurate distribution of negative and positive result values, which ultimately leads to a reduced grey zone (Area of Overlap) – an area that does not make it possible for us to decide clearly whether the test result is actually positive or negative.
Since TRISOMY test, TRISOMY test XY and TRISOMY test + are categorised under screening methods rather than diagnostic examinations, both false positive and false negative results may occur. A screen-positive result must therefore be diagnostically confirmed by any available diagnostic methods, i.e. by a genetic examination of the patient’s amniotic fluid.
A screen-negative result does not exclude the monitored trisomy types in absolute terms. There may be inaccuracies that are caused by naturally occurring phenomena, such as placenta mosaicism, vanishing twin syndrome, point mutations, gene inactivation, or other types of genetic or epigenetic mechanisms, or the presence of foreign DNA in maternal blood.
In a certain small percentage of cases, it is not possible to obtain a clear NIPT result. Such tests are considered unsuccessful.**** The failure may be caused either by technical or biological reasons. Such test failures are mainly caused by improperly obtained blood samples or improper transport conditions.
The most frequent biological reason for test failure is a relatively low proportion of foetal DNA in the obtained sample compared to the amount of maternal DNA. If the proportion of foetal DNA in the obtained sample is less than 4%, the reliability of the test drops significantly (Graph 5). According to the results presented by the studies published so far, the occurrence of samples with a low proportion of foetal DNA fraction ranges between 1.5-6.1%.
Results obtained by evaluating samples with foetal DNA proportions lower than 4% are not suitable for interpretation.
**** M. M. Gil, M. S. Quezada, R. Revello, R. Akolekar, and K. H. Nicolaides, „Analysis of cell-free DNA in maternal blood in screening for fetal aneuploidies: updated meta-analysis,“ Ultrasound Obstet. Gynecol. 45 (3), 249-266 (2015)