Newborns’ DNA reveals their gestational age

Breaking new ground 3. jul 2021 2 min PhD Kristine Løkås Haftorn Written by Morten Busch

It sounds trivial but is not at all that simple. Currently, determining the date of conception and therefore the expected due date is based on the parents’ statements about the woman’s last menstruation and on ultrasound imaging. Any deviations from normal fetal development become very important in research on how either preterm or post-term birth affects newborns. Now researchers have developed a method to determine the gestational age of newborn babies with greater precision based on a simple DNA sample and machine learning. The researchers hope over time to be able to determine gestational age in the womb and think that this knowledge will provide new insight into fetal development.

Most people calculate their age from the day they are born, but a person’s gestational age is calculated from the day they are conceived. Research on how preterm or post-term birth affects newborns requires determining this age as accurately as possible. A group of researchers therefore investigated this and developed a new method of determining gestational age at birth by analysing blood from the umbilical cord.

“Recent research has determined that the amount and distribution of small molecules called methyl groups that attach to DNA provide an accurate way of determining gestational age. We therefore used machine learning to identify 176 of the more than 850,000 possible locations of the methyl groups binding DNA. This method determines gestational age more accurately and gives us an opportunity to better understand the genetic and developmental stages of fetuses,” explains Kristine Løkås Haftorn, PhD Fellow, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo.

As accurate as a clock

The new method is based on modifications to human genome that leave the DNA code unchanged. This involves epigenetics (epi is Greek for outside) – small chemical modifications, in this case methyl groups that usually bind to one of the four chemical bases in DNA: cytosine (C). This often happens when cytosine is followed by guanine (G). Methylated sites are therefore often called CpG or CG sites, since the C-G DNA bases are linked by a phosphate group (p).

“Our genome has an estimated 28 million such CpG sites. Binding of the methyl groups to DNA can turn a specific gene on and off. This process of gene regulation is not random – especially in the fetal state, in which certain parts of the genome must be activated at different times in the various stages of fetal development,” says Kristine Løkås Haftorn.

The methylation patterns therefore occur at very precise times during fetal development and can therefore be used to determine the stage of pregnancy accurately – just like a clock that can show how long a pregnancy has lasted. To develop such a clock, the researchers studied newborns conceived by assisted reproductive technologies, since the exact time of conception was known for these pregnancies.

“We analysed the methylation pattern of the DNA in the umbilical cord blood when the children were born and found 176 characteristic CpG sites that were related to gestational age. To develop the clock, we trained the computer program on a group of newborns with known gestational age. We then used our clock to analyse 348 pregnancies conceived naturally and 838 pregnancies conceived by assisted reproductive technologies to determine whether we could calculate their gestational age accurately,” explains Kristine Løkås Haftorn.

Understanding fetal development and monitoring pregnancies

In addition to identifying a subset of CpG sites that were relevant to estimating gestational age, the researchers also used the new study to test a new methylation array – the Illumina Infinium MethylationEPIC Beadchip. Compared with the previous arrays that could only analyse 450,000 sites, this newer array is able to map almost twice the number of CpG sites (850,000). The precise location of the 176 relevant methylation sites can be important – not only for the new method but also for understanding fetal development.

“These 176 CpG sites show a characteristic pattern in relation to gestational age. We know that the timing of switching particular genes on or off is especially important for fetal development and believe that the CpG sites we have found in our clock can be used to better understand these mechanisms,” says Kristine Løkås Haftorn.

This finding could provide researchers with a wealth of information about when and why certain genes are turned on and off during fetal development. The researchers therefore want to study additional DNA samples from the children at several time points to find out how the methylation patterns change longitudinally. In the current study, they could only take samples at the time of birth, which thus only provides a snapshot of the methylation pattern at that specific time.

“This new method of determining gestational age will certainly prove to be an essential tool for many researchers around the world determining the effects of preterm and post-term birth. However, we also want to explore how to take samples non-invasively during pregnancy and thus get snapshots of methylation at several time points during pregnancy so that we can understand fetal development and monitor pregnancies better,” concludes Kristine Løkås Haftorn.

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