http://www.digitaljournal.com/tech-and-science/science/scientists-map-the-dark-matter-of-dna/article/477374

Scientists map the ‘dark matter’ of DNA

Posted Oct 16, 2016 by Tim Sandle
Understanding DNA variations can inform about health risks and it can also provide the basis for personalized medicine. There are still some knowledge gaps — which some call the ‘dark matter' of DNA.
The structure of the DNA
The structure of the DNA
Zephyris / Wikipedia
The revolution in genomics has revealed much about the structure and function of DNA and genes. There is, however, much still to learn especially in relation to DNA and disease. The majority of medical researchers think that larger structural variants within DNA play a key role in many hereditary diseases. The problem is that these variants are difficult to detect.
To examine this further, a research group from Saarland University studied the DNA of 250 healthy Dutch families against a DNA database. This formed part of the ‘Genome of the Netherlands’ project and it fits in the field of bio-informatics. Through this work, researchers have identified 1.9 million variants affecting multiple DNA 'letters'.
Among the variants are large sections of DNA which have disappeared or moved. When this occurs, the functionality of a gene encoded by DNA alters and this affects the protein that the gene produces. The impact of this is difficult to assess.
The research group describe two case studies where an additional piece of DNA has been detected outside the coding region of a gene. In both cases this affected gene regulation. Having pinpointed these effects the researchers hope to be able to predict large structural variants and how this leads to changes in our genomes. This will take further research, but the current study provides a starting point.
As well as variations, the research group discovered ‘extra’ parts of DNA and these may also affect protein production. One of these additional pieces has been described as a new "ZNF" gene, and this is predicted to occur in around 50 percent of the Dutch population. The gene, based on the reference database, is commonly found in various samples from the reference genomes of several species of apes. The function of this gene is unknown but it may have a role in genetic diseases.
The research is published in the journal Nature Communications, and it is titled “A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.”