Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Scientists develop method to standardize genetic data analysis

11.11.2019

MIPT researchers have collaborated with Atlas Biomedical Holding and developed a new bioinformatics data analysis method. The developed program, EphaGen, can be used for quality control when diagnosing genetic diseases. The team published the article in Nucleic Acid Research.

The mapping of the human genome in the early 21st century and understanding the nucleic acid sequence have provided ample opportunities for research on both genetic diseases and genetic predisposition.


DNA

Credit: MIPT Press Office

This has become possible after the development of next-generation sequencing, or NGS -- new methods for determining a DNA sequence. They produce faster results in a less costly procedure and can be integrated into routine clinical practice.

While the diseases that can be caused by defects in several distinct DNA segments -- called polygenic disorders -- are still the province of researchers, DNA diagnostics of single-gene disorders associated with a defect in a specific DNA segment (known as Mendelian disorders) is now a standard of care in medical genetics.

The main challenge when using NGS data in clinical practice is the need for an unambiguous answer to whether a patient has a mutation.

When a mutation is not detected, confidence that such findings are not associated with low data quality is required. Special quality metrics have been introduced to ensure this; however, they only provide indirect evidence of the presence or absence of a mutation.

Researchers from MIPT and Atlas have developed EphaGen software, which uses a new evaluation method to provide a straight answer to that question.

Given a spectrum of the clinically relevant variants of interest, it associates these NGS data with a single parameter. Based on the inner algorithm, this parameter resembles diagnostic sensitivity and may thus be used to decide whether the collected data are suitable for clinical interpretation or not.

"Interpretation of laboratory data has become more complex due to the rapid introduction of new sequencing methods in clinical practice," said the article's lead author, Maxim Ivanov, a PhD student at the MIPT Department of Bioinformatics.

"A doctor often wants a straight answer as to whether a mutation was detected or not. However, a laboratory is often unable to provide such an answer due to numerous 'buts.' Such as, 'We have not detected a mutation, BUT we haven't analyzed one gene, or the analysis of some genes was incomplete, or there was a technical failure in the analysis of certain regions of some genes.'

NGS is a large-scale technology, so a specific important DNA segment may remain unanalyzed, without this being noticed."

"We have implemented an integral characteristic that will enable a doctor to assess the reliability of the 'no mutation' result, and will provide a unified language for communication between a clinician and the laboratory. And of course, there can be numerous other applications, too. As we demonstrated in our study, it may assist labs to perform head-to-head comparison between different technical solutions or detect the source of failure, and so on," Ivanov added.

The developed EphaGen software provides a novel approach for performing measurement in routine clinical NGS testing and can be easily implemented into existing clinical workflows as a measure of quality control.

###

The research was conducted with the support of the Russian Foundation for Basic Research.

Media Contact

Varvara Bogomolova
bogomolova@phystech.edu
7-916-147-4496

 @phystech_en

https://mipt.ru/english/ 

Varvara Bogomolova | EurekAlert!
Further information:
https://mipt.ru/english/news/scientists_develop_method_to_standardize_genetic_data_analysis
http://dx.doi.org/10.1093/nar/gkz775

More articles from Life Sciences:

nachricht Detailed insight into stressed cells
05.12.2019 | Goethe-Universität Frankfurt am Main

nachricht State of 'hibernation' keeps haematopoietic stem cells young - Niches in the bone marrow protect from ageing
05.12.2019 | Universität Ulm

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: The coldest reaction

With ultracold chemistry, researchers get a first look at exactly what happens during a chemical reaction

The coldest chemical reaction in the known universe took place in what appears to be a chaotic mess of lasers. The appearance deceives: Deep within that...

Im Focus: How do scars form? Fascia function as a repository of mobile scar tissue

Abnormal scarring is a serious threat resulting in non-healing chronic wounds or fibrosis. Scars form when fibroblasts, a type of cell of connective tissue, reach wounded skin and deposit plugs of extracellular matrix. Until today, the question about the exact anatomical origin of these fibroblasts has not been answered. In order to find potential ways of influencing the scarring process, the team of Dr. Yuval Rinkevich, Group Leader for Regenerative Biology at the Institute of Lung Biology and Disease at Helmholtz Zentrum München, aimed to finally find an answer. As it was already known that all scars derive from a fibroblast lineage expressing the Engrailed-1 gene - a lineage not only present in skin, but also in fascia - the researchers intentionally tried to understand whether or not fascia might be the origin of fibroblasts.

Fibroblasts kit - ready to heal wounds

Im Focus: McMaster researcher warns plastic pollution in Great Lakes growing concern to ecosystem

Research from a leading international expert on the health of the Great Lakes suggests that the growing intensity and scale of pollution from plastics poses serious risks to human health and will continue to have profound consequences on the ecosystem.

In an article published this month in the Journal of Waste Resources and Recycling, Gail Krantzberg, a professor in the Booth School of Engineering Practice...

Im Focus: Machine learning microscope adapts lighting to improve diagnosis

Prototype microscope teaches itself the best illumination settings for diagnosing malaria

Engineers at Duke University have developed a microscope that adapts its lighting angles, colors and patterns while teaching itself the optimal...

Im Focus: Small particles, big effects: How graphene nanoparticles improve the resolution of microscopes

Conventional light microscopes cannot distinguish structures when they are separated by a distance smaller than, roughly, the wavelength of light. Superresolution microscopy, developed since the 1980s, lifts this limitation, using fluorescent moieties. Scientists at the Max Planck Institute for Polymer Research have now discovered that graphene nano-molecules can be used to improve this microscopy technique. These graphene nano-molecules offer a number of substantial advantages over the materials previously used, making superresolution microscopy even more versatile.

Microscopy is an important investigation method, in physics, biology, medicine, and many other sciences. However, it has one disadvantage: its resolution is...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

The Future of Work

03.12.2019 | Event News

First International Conference on Agrophotovoltaics in August 2020

15.11.2019 | Event News

Laser Symposium on Electromobility in Aachen: trends for the mobility revolution

15.11.2019 | Event News

 
Latest News

Swiss space telescope CHEOPS: Rocket launch set for 17 December 2019

05.12.2019 | Physics and Astronomy

Detailed insight into stressed cells

05.12.2019 | Life Sciences

State of 'hibernation' keeps haematopoietic stem cells young - Niches in the bone marrow protect from ageing

05.12.2019 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>