Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Mapping the 'dark matter' of human DNA

10.10.2016

Researchers from ERIBA, Radboud UMC, XJTU, Saarland University, CWI and UMC Utrecht have made a big step towards a better understanding of the human genome. By identifying large DNA variants in 250 Dutch families, the researchers have clarified part of the "dark matter", the great unknown, of the human genome. These new data enable researchers from all over the world to study the DNA variants and use the results to better understand genetic disease.

The findings were published on October 6 in the scientific journal "Nature Communications".

Although our knowledge of the human DNA is extensive, it is nowhere near complete. For instance, our knowledge of exactly which changes in our DNA are responsible for a certain disease is often insufficient. This is related to the fact that no two people have exactly the same DNA. Even the DNA molecules of identical twins have differences, which occur during their development and ageing.


This is a detail of a representation of a DNA variants map.

Credit: Nature Communications (DOI: 10.1038/ncomms12989)

Some differences ensure that not everybody looks exactly alike, while others determine our susceptibility to particular diseases. Knowledge about the DNA variants can therefore tell us a lot about potential health risks and is a first step towards personalized medicine.

Many small variants in the human genome - the whole of genetic information in the cell - have already been documented. Although it is known that larger structural variants play an important role in many hereditary diseases, these variants are also more difficult to detect and are, therefore, much less investigated.

... more about:
»DNA »dark matter »diseases »genomes

By comparing the DNA of 250 healthy Dutch families with the reference DNA database the researchers were able to identify 1.9 million variants affecting multiple DNA 'letters'. These variants include large sections of DNA that have disappeared, moved or even appear out of nowhere.

When this happens in the middle of a gene that encodes a certain protein, it is likely that the functionality of the gene, and thus the production of the protein, is compromised. However, large structural variants often occur just before or after the coding part of a gene. The effect of this type of variation is hard to predict.

In the paper two occasions are described in which an extra piece of DNA was found just outside the coding region of a gene. In these occasions the variants had a demonstrable effect on the gene regulation. This proves that even structural variants that occur outside the coding regions need to be monitored closely in future DNA screenings.

The catalogue of variants provided by this research enables other scientists to predict the occurrence of large structural variants from the known profile of the smaller ones. This technique opens new possibilities for studying the effects of large structural changes in our genomes.

Additionally, the research resulted in the discovery of large parts of DNA that were not included in the genome reference. This "extra" DNA does contain parts that could be involved in the production of proteins. One of the extra pieces of DNA that was described in the paper is a new "ZNF" gene that has previously never been found in humans. Nevertheless it appears to be present in roughly half of the Dutch population.

This particular gene is a member of the ZNF gene family that was known from the reference genomes of several species of apes. The new variant will now be added to the human reference database. Authors subsequently showed that this gene is also present in genomes of several other human populations, however its function remains unknown. The fact that these and other pieces of "dark matter" now have been placed on the genetic map enables scientists worldwide to study them and use the results to better understand human genetic diseases.

This study is part of the Genome of the Netherlands (GoNL) project. One of the main goals of the study is to map the genome of the Dutch population and all its variants. Several teams of bio- informaticians from different countries work continuously on the development of new algorithms for data analysis, as well as on innovative ways to combine existing algorithms. The result: an accurate representation of the genomes of the Dutch population and thereby a solid base for the personalised medicine of the future.

###

"A high-quality human reference panel reveals the complexity and distribution of genomic structural variants": https://doi.org/10.1038/ncomms12989

For more information on GoNL: http://www.nlgenome.nl/

ERIBA: European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
Radboud UMC: Department of Human Genetics, Donders Institute, Radboud University Medical Center, Nijmegen, The Netherlands
XJTU: Xi'an Jiaotong University, Xi'an, China
Saarland University: Center for Bioinformatics, Saarland University, Saarbrücken, Germany
CWI: Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands.
UMC Utrecht: Center for Molecular Medicine, Division of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands

Tobias Marschall | EurekAlert!

Further reports about: DNA dark matter diseases genomes

More articles from Life Sciences:

nachricht How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH

nachricht A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>