COVID-19 is a threat largely because scientists have a limited understanding of the disease. Alice Rathjen, a pioneer of computational biology and spatial analysis of genomes, proposed that a new method of studying genetic information could be the key in unlocking vital information about COVID-19 and other illnesses.
Rathjen was granted a seminal patent for mapping the genome in 2D and 3D in 2006 and has launched a company to use the digital mapping technology GIS or geographic information systems. She suggests that this new model of mapping could potentially help researchers understand COVID-19 better and develop treatments more quickly.
She adds that while researchers in the US and in Europe work hard to understand the genetic risk markers for COVID-19, the limited data available keeps them from achieving success. In fact, there were only 18 entities all over the world that were capable — and willing — to upload COVID-19 patient genomes for analysis. Hence, there are only fewer than 6,500 COVID-19 patients available for analysis despite the millions of cases worldwide.
Rathjen believes that the innovation she is working on would make it easier to analyze data by turning patient genetic information into a location data. Using existing GIS technology, researchers could then visualize risk factors and allow them to exchange genetic data.
How can researchers use GIS to understand COVID-19?
Rathjen states that genetic scientists have identified around 700 locations on human chromosomes that may be associated with the level of severity of COVID-19. However, they need a lot more genomes to confirm their studies. Thus, the more genomes available for study, the quicker they can pinpoint the location that a drug or a potential COVID-19 vaccine should target.
She adds that using GIS, the genomes could be published as web services that are shareable via the Internet, making data accessible worldwide without having to send it across countries. The collaboration layer is a feature present in GIS but not in bioinformatics tools. There would also be enough controls in the software that allow researchers to set up role-based access and determine the raw data being shared and the annotations that could be added.
Explaining it further, Rathjen states that researchers organize genetic data by location using a unique identifier. When those identifiers are mapped on one screen using GIS, the person’s genetic risk profile for COVID-19 and other diseases could be identified much more easily.
Currently, as part of the COVID-19 Host Genetics Initiative, researchers are examining the genetic information of those who have died of the disease. The data, as aforementioned, has been limited, but they have started identifying certain genetic markers associated with the severity of the patient’s response to COVID-19.
As there are going to be treatments and vaccines soon, there is a need to prioritize certain patient populations based on genomic risk. This information needs to be distributed quickly but in a controlled manner around the globe.
As for the specific details of Rathjen’s GIS technology for genome mapping, she explains that one DNA base pair is equal to 10 centimeters on earth because chromosome one is about 249 million units from the start to the end. In order to get it to fit inside the coordinate system, Rathjen divided the position on a chromosome by 10 and then moved it 100 million units to the west. Now, it can fit inside the map of the Earth.
An XY coordinate would then be created for the position of a base pair on a chromosome. Rathjen adds that her team has already taken the possible risk markers identified for COVID-19 and mapped them in GIS. But since it is a new approach, the technology would need to be validated by an official agency like the FDA or the CDC.
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