#genigmagame Looking for genome explorers to build the reference genome of cancer cells together.
A project is where you put forth your ideas for a specific area or scope. Collaborators make proposals to reach the goal of the project.
You can start debates, run a blog and conduct a survey. You can also set periodical meetings to make decisions about the project. You can start debates, run a blog and conduct a survey. You can also set periodical meetings to make decisions about the project. Some of these meetings are private and some are open. If they are open, it is possible to participate in them (for example: attending if the capacity allows it, adding points to the agenda, or commenting on the proposals and decisions taken).
Examples: A project for the betterment of urban drinking water, a project to reduce plastic use, etc.
At CNAG-CRG we are developing a game to explore the genomic alterations in cancer cells. Citizens and scientists will collaborate in building reference genome maps to understand the parts of the human genome that play a fundamental role in growth and development of cancer.
The human genome is a sequence of 3,000 millions letters. Its sequence and folding in the space determine how our cells work. We know that in cancer cells the rearrangements of the genetic material (e.g. chromosome translocations) occur and modify the “original” sequence. As a consequence, the contact regions between different parts of the genome are modified possibly leading to alterations in the vital functions of the affected cells.
Genigma is a game for smartphones to involve citizens in the cancer research. Its goal is to build genome reference maps for 4 different specific cancers using cell lines of breast cancer (T47D), bone cancer (U2OS), leukemia (KBM7) and cervix cancer (HeLa).
What is a genome reference?
The genome reference (since 2002) has been used as a base-line of all analysis done in human biology that requires a genome as a reference. However, this reference genome is one that was based on a healthy individual, which later has been corrected over the years to make it more general (less individual) towards an “average” white person. It is clear that this reference genome is good for normal cells BUT cannot represent the cell state of disease, even less of cancer.
We know that many cancers originated from changes in the genome, including large rearrangements in the genome. Therefore, individuals with cancer are likely to have in cancerous cells a genome that is not anymore similar to the reference genome.
One of the major advances in biology was the use of the so-called “cellular lines”, which allows to grow human cells in the lab and do experiments with them. There are several cell lines of cancerous cells, which are routinely used in laboratories world-wide and used to make assessments on the disease. Since most of the cancer research in the laboratory is done with cell lines, we need to have a reference genome for each of these cell lines. The generalized healthy reference genome is not good enough.
GENIGMA, through its players, addresses that problem by providing “computational power” as well as alternative solutions impossible to accomplish with deterministic algorithms. This can help to better define the reference genomes of cancer cell lines.
Each player will analyse various small fragments of the cancer cells’ DNA, that correspond to real data obtained in the lab. The reference genome will be obtained joining together these small fragments that collectively the players have analysed. This concerted effort will help us to discover which parts of the genome may play a crucial role in cancer development.
Game homepage: https://genigmagame.app/en/
To test the game you need to download the beta in your smartphone:
- for Androids, go to Playstore.
- For iOS, download Testflight and then look for Genigma there. You will not find Genigma in Apple Store at this moment.
Purpose of action
At the moment, Genigma is only open for beta testing. The official launch is planned for the end of September 2021.
More than 250 people have already participated in play-tests. Next play-test will be July 2021 with around 90 students participating in the "Barcelona International Youth Science Challenge (BIYSC)" organized by Fundació Catalunya La Pedrera.
In this new play-test, we aim to get citizens' help in identifying interesting regions within individual chromosomes. This information will guide us to study translocations between chromosomes. In previous play-tests, the players identified rearranged regions on chromosome 9 in the T47D breast cancer cell line. In this new test, we challenge students to play with fragments of chromosome 17 because we know from the scientific literature that there is a translocation between chromosomes 9 and 17 in T47D cells and we aim to discover how quickly and efficiently players can find those regions.
In the future, citizens will have the entire genome of these cells at their disposal and it will be in their hands to discover new alterations currently unknown to science, information that will be of great use in advancing scientific knowledge and more targeted treatments.
For more information about participation in Genigma project you can contact the scientific team here: https://genigma.app/en/contact/