Increased ease of archiving, analyzing and interpreting genomic information. This is the challenge for engineer Idoia Ochoa, whose research focuses on developing digital formats and algorithms that make personalized medicine a reality.
In 2009, Ochoa left behind techno, Faculty of Engineering of the University of Navarra, to fly to the United States with a scholarship from LaCaixa. There he completed a master’s degree and a PhD at Stanford UniversityI went through companies like Google and worked as a professor at the University of Illinois.
In 2020, she returns to Technon, this time as a teacher, to continue her research work and share her knowledge and experience with new generations of students. We spoke with her about all the possibilities that genomic data offers for advancing personalized medicine and fighting diseases like cancer.
What do genome data tell about patients?
The genome can give us a lot of information about diseases, both the ones we can suffer from and the ones we already have. On the other hand, the DNA study From healthy cells, it is possible to detect whether there is a predisposition to developing certain diseases or problems. This information can be consulted at any time to work on prevention issues.
In addition, the diseased cell’s genome gives us other clues. Studying how the genome of cancer cells changes in a particular condition helps determine which treatments might work best and assess whether the disease is more or less aggressive, for example.
All this data provided by the genome must be processed and analyzed. This is where your search comes in.
Effective way. Through my work I try to make dealing with genetic data easier and easier. We develop tools to store them efficiently and take up minimal space. We also make it easy to access only certain data during investigations, without having to download the entire file, and to insert annotations into the file itself without having to obtain additional documents.
Another branch of my work focuses on improving data analysis. We develop tools for software and algorithms that allow clinicians, biologists, and researchers to perform some procedures that were hitherto not possible.
What are the benefits of these solutions?
Having effective data storage and management tools saves time for the researcher. It makes it possible to locate, download and share them faster, for example. In addition, the development of new algorithms allows to perform other types of analysis and to improve those that already exist.
From our recent articles in Nature Communications refers to mos, a new tool with which several different samples of genomic data from a tumor can be analyzed together. This provides a lot of information and a more complete picture of the disease. Until now, all samples had to be analyzed separately. As a result, there was a gap when performing this type of analysis, because it is very costly to sequence a tumor multiple times.
The ultimate goal of all this is to create personalized medicine. What are its features?
First of all, personalized medicine helps the patient. In cancer treatments, knowing the differences in the genome allows doctors to directly give the best treatment. You never know one hundred percent that it will work, but it increases the chances.
“In cancer treatments, knowledge of differences in the genome allows clinicians to directly give the best treatment”
What has been done so far is to try different treatments until the right one is found, without taking into account all these clues provided by the genomes. This wastes money, resources and valuable time for the patient.
When can we get a personalized medicine like the one you develop with your tools?
It depends. Each disease must be studied separately, because they are different and have their own peculiarities. There are diseases in which allocation takes place quickly and others in which the process is slower because of less money, research, or less attention. The breast cancerFor example, in the first group. It is a much-studied disease. There are already tests that allow DNA to be sequenced and to identify the people most willing to develop it.
So, I won’t say when we can have personalized medicine, but it’s already a reality for some diseases. Today, genomics information is already used for decision-making, and as progress continues, it will be more and more present today.
Another goal of your research is the ability to share information. Are we moving toward a more collaborative kind of medicine?
In general, participation tends to be maximal, which is important because data is required to advance in many areas. Without it, you cannot check if your ideas are working and explain them later.
“To move forward in many areas, what you need is data. Without it you cannot check if your ideas are working and prove them later.”
Except in exceptional cases, the tools are freely available to facilitate investigations. Many open databases are created, as are private ones, but they allow you to access them if you need the information to investigate.
Projects like Moss facilitate early diagnosis. Will medicine increasingly focus on improving and accelerating diagnosis?
There are several factors at play here. First, prevention. Knowing that you are prone to certain diseases guides you to change your habits and take care of yourself. Once you have the disease, early detection is important. Analyzing genomic data can help spot problems faster.
Finally, there is the treatment. When someone is verified as having a disease, the question arises: Can we use information from the genome to provide a more personalized treatment for that person? In many cases, the answer will be yes. This is very positive. Above all, for the patient, although it also saves financial resources and makes health systems more efficient.
What role does technology play in all of this?
It is essential. For data analysis in general and the study of genomes in particular, the development of technology and algorithms are what make the hack possible. Without them, it would be unreasonable to analyze such large amounts of information
To develop some of our tools that we rely on machine learning And deep learning. Others like Moss rely on theoretical developments and more probabilistic methods, which we apply later in a software.
The United States has been replaced by Spain. How do you see the present and the future of research in our country?
I think more and more research is being invested in Spain, especially in societies like the Basque Country and Catalonia, but there are still many differences with the United States. One of the obstacles we find when returning to Spain after obtaining a doctorate and working as professors abroad is the scarcity of a job offer. It is difficult to find a job in the public university, there are not many scholarships and there are not many offers in the private sector.
This is a big difference from the United States. When I decided to do my PhD in Spain, everyone asked me if I wanted to become a teacher. It seems that there are no other exits. I found at Stanford University that very few researchers remained at the university. They went to big companies like Google or Facebook or set up their own companies.
“Spain has very good researchers, but it is necessary to improve the linkage between PhDs, companies and research”
Here, academic training and doctoral experience are not valued outside academia. Spain has very good researchers, but there is still a need to improve the interrelationship between PhDs, companies and research.
Another important difference with the US is that, there, researchers are encouraged to combine Ph.D.s with internships in companies. I was a summer at Google and another at a start. This is useful for a doctoral student because it allows him to test the areas in which he prefers to work. And for companies, they have the possibility to meet potential employees. Often these practices end with job offers on the table.
There is another aspect that needs to be improved and that is conciliation. In your experience, is this possible?
I can send a positive message and say yes. I have three young daughters who were born in the United States and who are now back in Spain. I think it is possible to be a mother, to work and to be a leader in what you do if the necessary facilities are provided.
In this sense, COVID-19 has helped spread remote work and there is more flexibility. This is another difference with the US, where work, at least in my sectors, is measured by results and there is not much obsession with schedules as long as goals are achieved. I think this is necessary so that families, especially women, can get the profession they want.
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