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RCMG experts developed and registered their own software for NGS

The FSBI Academician N.P. Bochkov Research Centre for Medical Genetics was one of the first in Russia to introduce NGS methods into clinical practice and use them in their daily work to diagnose patients with suspected genetic diseases.

Next-generation sequencing (NGS) is a method that allows reading gene large regions, as well as the entire genome of several patients simultaneously. The procedure is much faster than Sanger sequencing, which "reads" each individual gene.

In some cases, the former methods would not allow a close study of several genes or dozens or hundreds of genes causing diseases with similar symptoms in a short period. It was even difficult to sequence large genes, such as DMD, the dystrophin gene. “With NGS, we can do this,” Oksana Ryzhkova explained, the Head of Genome Shared Resource Centre at RCMG, “in a number of cases, only genetic testing allows us to establish an accurate diagnosis. Many diseases are similar in their manifestations, and it is practically impossible to distinguish them only by their clinical picture. As a result, when we make a diagnosis without using DNA diagnostics, there is a possibility of making an incorrect diagnosis and prescribing the wrong treatment. NGS allows us to diagnose quickly and accurately.”

Experts receive a large amount of data when using the NGS method. Thus, the study of a small panel of genes (a list of genes, which mutations can trigger a disease development) identifies several dozen genetic variations from a single patient. Sequencing of the full exome (the largest genetic panel including all the genes encoding proteins) provides information on 30,000 variations from one patient, while analysis of the full genome shows 3 million. Today, geneticists need to look through a large number of databases to determine the pathogenicity of mutations they found, but this process is too long and complicated without software. The new software allows the automatic search for appropriate variations in all of the databases. This brings almost to zero the risk that the specialist will miss the right variant.

In addition, the new software prevents sequencing errors that inevitably arise during operation.

“Various equipment and reagents are used for sequencing. Different types of errors accumulate depending on the platform the laboratory uses," explains Oksana Ryzhkova. "Sequencing errors can be mistaken for pathogenic mutations. Therefore, to assess the identified variations, experts need to consider information about previous studies performed under the same conditions. Our own software means no time is wasted interpreting such sequencing errors and excludes the chance that they will end up in the conclusion. This is extremely important.”

The new in-house developed software allows use of the latest versions of analytical programs for data processing, as well as their timely update and activations of the most relevant genetic databases. The new software main advantage is that it takes into account Russian specifics. It allows accumulating and processing information on the frequency of hereditary diseases in Russian regions for further scientific and medical use.

RCMG is the national leading medical genetic institution; it has accumulated a large amount of unique data during its 50 years of operation. In 2020, the RCMG experts performed more than 55,000 genetic studies.