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Taking the detection of foetal chromosome disorders to the next level

2019_08_26_TAC_seq (unsplash.com)
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Estonian bioinformaticians together with geneticists developed an advanced data analysis method, which in addition to the foetal chromosome disorders, now also identifies the origin of the error, i.e., whether the chromosomal abnormality is of maternal or paternal origin. The new method promises to make the incredibly precise and safe foetal chromosomal analysis NIPT more available to patients. The scientists now need to continue the development to take the innovations from the laboratory to clinics.

A continued increase in the age of pregnant women also increases the risk for foetal chromosome disorders, such as Down syndrome, and raises an urgent need for discovering the abnormality early in the pregnancy. The modern NIPT (Non-Invasive Prenatal Testing) test enables to detect the most common foetal chromosome disorders from the mother’s blood sample with an accuracy of around 100 per cent. Even though NIPT is available in all women’s clinics in Estonia, not every family can afford it at its current price of €250.

Researchers from the Competence Centre on Health Technologies (CCHT) in collaboration with the University of Tartu and the University of Helsinki developed novel software for data analysis, which will make it possible to develop a significantly more affordable NIPT test. Similar to the current test, the new methodology will use modern DNA sequencing technology for analysing the foetus’ cell-free DNA found in the mother’s blood sample. However, while you cannot choose which chromosomes you want to study with the current NIPT tests, the new method makes it possible to target only the chromosomes most frequently causing chromosomal diseases.

The research recently published in PLOS ONE gives a detailed description of the inner workings of the analysis and shows how the modern machine learning methods of data analysis can be applied in healthcare. The new NIPT methodology currently under development is being patented by scientists.

The lead author of the research, a research fellow of bioinformatics and genomics at the Institute of Genomics of the University of Tartu, Priit Palta, explained that the developed data analysis framework was the missing link in developing more affordable NIPT tests. “The reliable and early detection of foetal chromosome abnormalities from the mother’s blood sample is and will be a challenge in data analysis. For example, in the case of Down syndrome, the foetus has three copies of the 21st chromosome instead of two, but as the proportion of foetal DNA in the blood sample of a pregnant woman is limited, the difference in DNA sequencing data is invisible to the naked eye. However, the sensitive data analysis methodology finds these differences relatively easily and shows them in the NIPT report with high confidence.”

Palta explained that in addition to detecting chromosomal abnormalities, the new analysis method can also identify the origin of the error, i.e., evaluate whether the trisomic chromosome is of maternal or paternal origin. In situations, where chromosomal abnormalities are repeated in children or pregnancies, this information may be of utmost importance for parents and doctors when planning to have more children.

According to the head of the Precision Medicine Laboratory of the Competence Centre on Health Technologies and a research fellow at the University of Tartu, Kaarel Krjutškov, practical fundamental research needs to be continued at the lab. “A specific data analysis package is essentially a multi-level machine learning solution developed with the need for a sensitive and more affordable NIPT test in mind,” said Krjutškov.

Krjutškov also pointed out the importance of collaborating with the university and the need to value fundamental research, as the implementation of its results is available to the patients at clinics. “The novelty of this approach is confirmed by the fact that one of the leading authors of the analysis, a doctoral student of bioinformatics at the Faculty of Medicine of the University of Tartu, Hindrek Teder, is defending his doctoral thesis based on this research article. There are not many young researchers in the world that would defend their doctoral thesis on the topic of developing the NIPT test as precision medicine in use in clinics.”

More information:

Link to the article https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0209139

Kaarel Krjutškov, PhD, Head of the Precision Medicine Laboratory at the Competence Centre on Health Technologies, Research Fellow at the University of Tartu and the University of Helsinki, +372 5126 416, Kaarel.krjutshkov@ccht.ee

The translation of this article was funded by the European Regional Development Fund through Estonian Research Council.

Picture by: Unsplash.com

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