New molecular engineering method improves precision of biomarker analysis

Bioinformatics

The new molecular engineering method, called TAC-seq, raises the precision of biomarker analysis and is poised to make it more affordable. The method, for which a patent is pending, will be introduced in the healthcare system this year in the form of endometrial receptivity test.

Researchers from the University of Helsinki in cooperation with the University of Tartu, Competence Centre on Health Technologies from Estonia, and the Karolinska Institute, published an article in Nature’s partner journal Genomic Medicine in which they present Targeted Allele Counting by sequencing (TAC-seq) along with several of its potential applications.

The method measures, at an extremely high level of precision, the number of DNA and RNA molecules used as biomarkers in clinical samples and thereby describes the patient’s state of health.

A biomarker can be any molecule whose existence or absence is measurable and which gives information about the state of health. Clinics use thousands of biomarker-based tests, of which many analyse DNA as an agent of heredity, and gene expression profiles. It is imperative that responses to clinical testing are as precise as possible and that the testing be priced at a reasonable level.

“Ordinarily, in clinical samples, the DNA has to be amplified using the polymerase chain reaction method to ensure material for the next-generation sequencing, otherwise it isn’t measurable by instruments. However, it is not known how many copies are created of a given original molecule and thus the results are inaccurate. With TAC-seq, we can identify and remove all of the artificial copies made in the lab, and the corrected biomarker values reflect the clinical sample with maximum reliability,” says the first author, doctoral student in University of Tartu Bioinformatics Hindrek Teder.

The researchers introduce three possible applications for the method. First of all, TAC-seq can be used for the endometrial receptivity testing – determining the levels of specific RNA molecules with the aim of ascertaining the best possible time to transfer the embryo during infertility treatment and thereby increase the likelihood of success of in-vitro fertilization (IVF).

The method can also be used for non-invasive prenatal genetic testing to study the cell-free DNA in the woman’s blood to detect the most common chromosomal disorders in the fetus. Third, the method can be used for precise microRNA profiling in different body fluids. These molecules can be used as biomarkers for several conditions and thus forgo the need to perform a biopsy.

TAC-seq based endometrial receptivity test has reached validation at private clinics in Helsinki and Turku.

“Advanced and precise diagnostic tools help women with recurrent implantation failures. We see that the implantation window is different in patients and should be taken into account in IVF treatment. The general IVF quality could be improved if individual embryo transfer timing and drug dosage are taken into account,” commented Tiina Hakala-Ala-Pietilä, Specialist in Obstetrics and Gynaecology.

The leader of the study, Dr Kaarel Krjutškov from the University of Helsinki and in Competence Centre on Health Technologies, notes that there has been a pressing need for an ultra-precise and affordable solution, and TAC-seq will broaden the possibilities in research laboratory and in clinics.

“First we conducted thorough fundamental research, then we filed for an international patent. Now we have published our results, describing the various facets of the method’s applications and the most important thing – the method is in progress of integration into the healthcare system.”

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