Nav: Home

Scientists develop method to standardize genetic data analysis

November 08, 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. 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.
-end-
The research was conducted with the support of the Russian Foundation for Basic Research.

Moscow Institute of Physics and Technology

Related Bioinformatics Articles:

Embracing bioinformatics in gene banks
Scientists from the IPK have explored, within a perspective paper, the upcoming challenges and possibilities of the future of gene banks.
New bioinformatics tool identifies and classifies CRISPR-Cas systems
Designed to improve the utility and availability of increasingly diverse CRISPR-Cas genome editing systems, the new CRISPRdisco automated pipeline helps researchers identify CRISPR repeats and cas genes in genome assemblies.
AMP Iissues consensus guideline recommendations for NGS bioinformatics pipelines
The Association for Molecular Pathology, the premier global, non-profit molecular diagnostics professional society, today published 17 consensus recommendations to help clinical laboratory professionals achieve high-quality sequencing results and deliver better patient care.
A new tool to decipher evolutionary biology
A new bioinformatics tool to compare genome data has been developed by teams from the Max F.
Advances: Bioinformatics applied to development & evaluation of boron-containing compounds
The interest for developing boron-containing compounds as drugs is increasing after some successful cases.
When life sciences become data sciences
The University of Freiburg offers Europe-wide infrastructure and service in Bioinformatics.
Bioinformatics brings to light new combinations of drugs to fight breast cancer
A bioinformatics analysis of pairing 64 drugs used to treat breast cancer allows researchers at IRB Barcelona to identify 10 previously untested combinations with potential to tackle resistance to breast cancer treatment.
New bioinformatics tool tests methods for finding mutant genes that 'drive' cancer
Computational scientists and cancer experts have devised bioinformatics software to evaluate how well current strategies distinguish cancer-promoting mutations from benign mutations in cancer cells.
EDGE bioinformatics brings genomics to everyone
A new bioinformatics platform called Empowering the Development of Genomics Expertise (EDGE) will help democratize the genomics revolution by allowing users with limited bioinformatics expertise to quickly analyze and interpret genomic sequence data.
VirusDetect, a new bioinformatics pipeline for virus identification released
A new bioinformatics analysis tool developed by researchers at the Boyce Thompson Institute can help scientists to identify all known and novel viruses and viroids within small RNA datasets on a local to global scale.
More Bioinformatics News and Bioinformatics Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Teaching For Better Humans 2.0
More than test scores or good grades–what do kids need for the future? This hour, TED speakers explore how to help children grow into better humans, both during and after this time of crisis. Guests include educators Richard Culatta and Liz Kleinrock, psychologist Thomas Curran, and writer Jacqueline Woodson.
Now Playing: Science for the People

#556 The Power of Friendship
It's 2020 and times are tough. Maybe some of us are learning about social distancing the hard way. Maybe we just are all a little anxious. No matter what, we could probably use a friend. But what is a friend, exactly? And why do we need them so much? This week host Bethany Brookshire speaks with Lydia Denworth, author of the new book "Friendship: The Evolution, Biology, and Extraordinary Power of Life's Fundamental Bond". This episode is hosted by Bethany Brookshire, science writer from Science News.
Now Playing: Radiolab

Dispatch 3: Shared Immunity
More than a million people have caught Covid-19, and tens of thousands have died. But thousands more have survived and recovered. A week or so ago (aka, what feels like ten years in corona time) producer Molly Webster learned that many of those survivors possess a kind of superpower: antibodies trained to fight the virus. Not only that, they might be able to pass this power on to the people who are sick with corona, and still in the fight. Today we have the story of an experimental treatment that's popping up all over the country: convalescent plasma transfusion, a century-old procedure that some say may become one of our best weapons against this devastating, new disease.   If you have recovered from Covid-19 and want to donate plasma, national and local donation registries are gearing up to collect blood.  To sign up with the American Red Cross, a national organization that works in local communities, head here.  To find out more about the The National COVID-19 Convalescent Plasma Project, which we spoke about in our episode, including information on clinical trials or plasma donation projects in your community, go here.  And if you are in the greater New York City area, and want to donate convalescent plasma, head over to the New York Blood Center to sign up. Or, register with specific NYC hospitals here.   If you are sick with Covid-19, and are interested in participating in a clinical trial, or are looking for a plasma donor match, check in with your local hospital, university, or blood center for more; you can also find more information on trials at The National COVID-19 Convalescent Plasma Project. And lastly, Tatiana Prowell's tweet that tipped us off is here. This episode was reported by Molly Webster and produced by Pat Walters. Special thanks to Drs. Evan Bloch and Tim Byun, as well as the Albert Einstein College of Medicine.  Support Radiolab today at Radiolab.org/donate.