INTRODUCTION: WHAT INSPIRED ME FOR THIS PROJECT
The COVID-19 coronavirus is currently causing a pandemic. And the curious thing and unlike other epidemics or pandemics is that it is being seen that this virus does not affect all patients equally, regardless of their age and causing some common symptoms, thus we can find young and healthy patients (without pathologies) who, when falling ill with COVID-19, reach extreme severity or clinical involvement, and may die, while other young or elderly patients manage to recover in a healthy way. more or less easy.The research community worldwide is beginning to study or analyze the genome of these patients, trying to find a possible explanation for this heterogeneous clinical response in genetic susceptibility or in the existence of mutations or variants in certain risk genes. or candidate genes of the highest susceptibility to the disease, or in other genetic and genomic anomalies that could cause greater involvement in some patients and not others. A gene that could be implicated in or influence this greater susceptibility or involvement to COVID-19 infection has already been identified, such as the ACE2 gene, but it is further study and analysis at the genomic level of these patients is necessary. On the other hand, greater in-depth knowledge of the molecular mechanisms involved in this disease (with the contribution of bioinformatic analysis) will allow finding the most appropriate treatment for each case. Furthermore, we have also in our team with a specialist in nutrigenomics ,working on the study of gene-nutrient interaction and modulation of the epigenome by nutrients,then WE CAN ADD THE NUTRITIONAL ENVIRONMENT TO THE STUDIO/PROJECT. This COVID-19 pandemic occurs in a poor diet nutritional environment with deficiencies of basic nutrients for the immune system. Studies published to date indicate that diabetes and hypertension, both related to nutrition, are risk factors for a poor prognosis of the disease. And the prevalence of obesity is high among the youngest patients with the worst progression. Bioinformatics is a discipline that can contribute and greatly help the study and research of human diseases, based on the massive sequencing of the genomes and transcriptomes of the affected patients to study. I have training in bioinformatics, as well as 8 years of experience in bioinformatic analysis of the human genome and transcriptome from massive sequencing, applied to the study and research of various human diseases, and therefore I propose this project together with a multidisciplinary team of bioinformaticians, a computer engineer specializing in data analysis, a nutrigenomic expert and a microbiologist. We will use and need the FASTQ massive sequencing files of patients suffering from COVID-10 to analyze them bioinformatically, interpret the results and thus identify the causes of this. heterogeneous clinical response in seriously ill patients, in order to propose their best treatment and adequate preventive measures based on these causes.
THE PROBLEM WE WILL SOLVE
COVID-19 IS HETEROGENEUS AND SELECTIVE IN THE CLINICAL RESPONSE IT INDUCES IN PATIENTS and some patients are more susceptible than others, and may even die,regardless of age and good health prior of the patient. How important is the problem? Currently the problem has no solution or prevention because it still is not known the etiology or molecular mechanism of this clinical heterogeneity and selectivity.
THE SOLUTION WE BRING
The best solution is the BIOINFORMATIC ANALYSIS OF GENOMIC DATA from massive sequencing of COVID-19 patients (their DNA and RNA FASTQ files), as well as the correct interpretation of the results of this analysis, which WILL ALLOW CONCLUSIONS to be drawn and TO BE IDENTIFIED THE CAUSES of this heterogeneity and selectivity in the clinical response of some patients. And thereby adapt or seek THE BEST POSSIBLE TREATMENT (PERSONALIZED MEDICINE) and the most appropriate PREVENTIVE MEASURES in the future for different types or groups of patients that carry those causes or genetic/genomic abnormalities that we are going to detect. It is necessary and essential to do MASSIVE sequencing of these patients since it allows us to analyze all the genes of their genome and with it identify the group of genes or genomic regions that influence this exaggerated clinical response of some patients and that we know today, as in almost all diseases, not caused by a single gene or marker but by a network of genes. UNTIL NOW THIS SOLUTION HAS NOT BEEN IMPLEMENTED AND IT NEEDS TO BE DONE NOW.Any other possible solution would be only a partial solution to the problem.OUR PROJECT IS FULLY VIABLE AND USEFUL FOR THE COVID-19 PATIENTS
The objetives or phases of our project are: 1) Bioinformatic analysis of genomic data of different types / groups of COVID-19 patients with different pathologies (diabetes, hypertension, obesity, cardiovascular risk, cancer, etc.) vs. Non-COVID-19 patients, for identify the causes of the different clinical response to COVID-19 infection in the different patient groups.Genomic data comes from sequencing of patients admitted to hospitals, with their permission or consent to use, and may also come from public repositories and from other colaborating interested projects. 2) Nutrigenomic study of patients, knowing their nutritional environment, to see the possible influence of nutrition, gene-nutrient interaction and modulation of the epigenome by nutrients in improving the clinical response to infection by COVID-19. 3) Search for the most suitable therapies for the different patients and the best recommended preventive measures for the future and for future patients of COVID-19, based on the causes identified in point 1.
WHAT YOU HAVE DONE DURING THE WEEKEND
I have formed and coordinated my team to properly prepare the pitches, talking to each other to make the project better and more complete.And also I tried contacting with persons of another projects related with our project for the availability of genomic data of COVID-19 patients.
THE SOLUTION'S IMPACT TO THE CRISIS
The solution's impact to the crisis in our case will be big,because with our solution we can avoid and prevent deaths of some patients more susceptible to worsening.
THE NECESSITIES IN ORDER TO CONTINUE THE PROJECT
1) We have calculated and estimated a budget of informatic infraestructure needs if our project continues, that can be seen into the upload files we attach (a word file named as Budget_COVID19PATGENOME.doc).
2) We will need from all possible sources the genomic data (DNA and RNA FASTQ files) from COVID-19 patients with different pathologies, and from the non-COVID-19 persons (controls).
THE VALUE OF YOUR SOLUTION AFTER THE CRISIS
The solution of our project is perfectly scalable,adaptable and applicable to other similar environments of human diseases or similar pandemics, because our bioinformatic methodology is already proven in multiple studios and scientific works, as you can see in the scientific literature.It is a methodology with future.
THE URL TO THE PROTOTYPE
Our project, because is basically a bioinfornatic project has not a prototype but rather a PROTOCOL or workflow of the inputs files (FASTQ files of COVID-19 patients), that can be seen in the next URLs :