Genomic medicine
Genome Medicine
Tim Hubbard, Serious Science
Translation: Irina Lineva, Post-science
Bioinformatician Tim Hubbard on the project "100,000 genomes", how to use genetic data in the diagnosis and treatment of diseases and what difficulties are associated with the use of genomic medicine.
Genomic medicine is the use of a patient's genetic data in treatment. For many years, scientists have sequenced the genomes of animals, such as a mouse or a danio-rerio fish, which were also important for human research. How genetic data will help in the treatment and diagnosis of diseases, says bioinformatician Tim Hubbard.
Genome sequencing and disease treatment
In 2006, a new sequencing technology appeared, and it became clear that the cost and time of genome sequencing could be significantly reduced. Right now, full genome sequencing costs less than a thousand dollars and takes about a day using a single machine. We have suddenly moved from the data of a single genome to the ability to collect data on the genomes of many people for a fairly standard price for healthcare.
Around 2009, the British House of Lords published a report on genomics in the health service and recommended that the government begin to study whether this technology could be used to improve medical care. A few years later, a government report appeared, and this marked the beginning of the 100,000 Genomes project, which was launched in 2012. Genomics England was established in 2013 to carry out the project.
So, how can knowledge about the human genome be applied in healthcare? There's one thing we can't do for sure: we don't understand the workings of genes well enough to predict a person's future. This information is simply unreliable. But if we know that you suffer from certain diseases, and there is a suspicion that they are related to your genes, now a number of individual tests can be carried out in the UK. We introduced them a few years ago. This is a corpus of about 800 tests for specific genes. But if this does not give us the necessary information to make a diagnosis – and we can make a diagnosis in 15-20% of cases – then if we sequence the entire genome, we can study it and see where else the problem may be hiding.
Now it is quite cheap, and such a practice can be implemented into the healthcare system – in the last five years, the 100,000 Genomes project has been doing just that. As for rare diseases, you can compare the genomes of a patient and his parents, and if a person has cancer, then compare the genome of cancer cells with normal ones. On based on these analyses performed for specific patients, it is possible to compile a report that will help doctors choose the most appropriate drug.
Often, patients with rare diseases have been examined in the health care system for many years, but they have not been able to determine exactly what violations occurred in their body. If you sequence the entire genome, you can pretty accurately determine what is wrong, which genes are associated with it, and in some cases, make a treatment regimen that initially would not have occurred to you as a doctor.
I'll give you an example: one girl started having epileptic seizures at the age of four, and we didn't understand what was wrong with her. It turned out that the problem is in a gene that is associated with the transport of glucose to the brain. Thus, the problem was not related to the brain, but to energy exchange, and for the girl it was necessary to choose another diet in which glucose is not involved. The girl did not recover completely, but she began to feel well, as the nutrition of the brain improved. Such unexpected results can be obtained in a situation where the doctor initially could not make a diagnosis, but as a result he receives accurate information about which processes were disrupted at the molecular level.
Genomic Medicine Service
The project was launched five years ago, and its goal – to sequence one hundred thousand genomes – has already been achieved. We collected data on how genetic information helped doctors, and it was decided that genome sequencing would continue to be used in healthcare as part of a standard patient treatment program: initially, the project was only supposed to establish how useful this method was. Now the so-called genomic medicine service will appear throughout the UK. In London, it will be handled by the Royal College Hospital – it will be a leading laboratory, one of the seven centers for genetic research. In the future, people with rare diseases or oncology will be able to contact one of the laboratories to decode their genome for clinical purposes, if this proves to be the best way to get the information needed for treatment.
Of course, the good thing about working with the human genome is that it does not change over time: it is enough to sequence it once, and then you can turn to it at any time in search of the cause of a particular disease. At the moment, we only sequence the genome of those who are already sick, but if you were sick once, we received your genome and you returned to us with another disease, we will not have to sequence it again. Most likely, this approach to the use of genetic data will become universal.
Other possibilities open up to us, for example, pharmacogenomics, which allows you to choose the most effective drug for you for a particular disease. Now we do not conduct special tests for the selection of medicines, and usually the doctor prescribes you some drug, and if it does not work, prescribes another. But if we look at your genome, in some cases we can immediately determine which drug is best for you and in what dosage. Thus, the application of genomics can help us systematically improve healthcare.
Prospects of genomic medicine and open questions
The next phase of the project is to sequence the genome of 500 thousand patients, and possibly 5 million patients over the next five years. In addition to working at King's College London, I am engaged in the company Genomics England and participated in the organization of the project for all five years. Genetic information can be used directly to help patients, but one of the goals of our project is to use this data for research purposes as well.
We cannot distribute them, as this is confidential information: patients must be sure that their health information is reliably protected. But we can set up the system so that researchers can come to a secure computer environment for analysis and help us improve patient treatment regimens, since we do not understand the nature of their diseases in all cases. Sometimes researchers working with genetic information can help us interpret the data obtained and find an explanation of why the problem arose. This research activity is part of our work.
Our knowledge in the field of genomic medicine is rather scarce: we cannot predict what health problems you will have, we cannot even reliably predict the occurrence of diseases such as breast cancer. We know that BRCA1 or BRCA2 genes are major risk factors, but we understand too little about them even. In addition, it makes sense to test for them only if you have already had cases of breast cancer in your family: if there were none, the data obtained about these genes for the healthcare system is not reliable enough and does not have sufficient predictive power. So we should improve our ability to interpret data and differences in genomes. Right now, our capabilities in this area are extremely limited.
About the author: Tim Hubbard – Professor of Bioinformatics, King's College London.
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