Skip to 0 minutes and 11 seconds In Birmingham we had a large outbreak of Salmonella in a local hospital. And that’s very unusual - salmonella is a very common infection but it usually affects people in the community who have picked it up from contaminated food - particularly things like chicken and eggs. So one of the key questions for doing whole genome sequencing rapidly is to really understand what’s going on in the hospital. With genome sequencing you get a whole picture. You can see as little as a single mutation in the five million base pairs that make up the salmonella genome. And that signature is enough to say whether something is part of an outbreak or not.
Skip to 0 minutes and 55 seconds The outbreak was controlled in the hospital and the problem went away. This same type then started to be detected in France and Germany and in Europe. So in fact what we were able to do with genome sequencing was to trace back through the food distribution network to an individual producer of eggs in Germany who maintained three chicken farms. The genetic information mapped beautifully onto the three chicken farms owned by this producer.
Skip to 1 minute and 26 seconds There are a large number of people with undiagnosed genetic conditions and rare diseases in whom we suspect the condition is genetic but we don’t actually know the gene responsible. The aim is to analyse all of an individual’s genetic information in order to try and find the cause of their rare disease.
Skip to 1 minute and 47 seconds Blood samples were taken from Jessica and both parents. And as a result of analysing all of their genes it was determined that there was one tiny change in one of Jessica’s genes that was not present in either parent. And, looking at what we know about this gene, we could see that it did fit with Jessica’s clinical features of developmental delay and epilepsy. And this is a particular type of epilepsy which occurs because the brain doesn’t get enough glucose from the diet. The gene that’s not working in Jessica is responsible for making a protein that allows glucose to be transported into the brain from the blood. In Jessica’s case this doesn’t work properly.
Skip to 2 minutes and 36 seconds The importance of this diagnosis is that we know that this particular type of epilepsy responds very well to a ketogenic diet. This is a special diet that uses an alternative form of energy - ketones to provide the brain with the energy it needs to function normally. As a result of this, Jessica’s anticonvulsant medicine can be tailed down and the ketogenic diet can be introduced with what we hope will be a good effect.
Skip to 3 minutes and 9 seconds For cancer, whole genome sequencing is being used but it’s being used more in the area of research than for actual diagnostics at the moment in patients. This is because if we were to use whole genome sequencing to look at patient samples the answers that we can get from it we can actually get from doing targeted panel screening at the moment. But the exciting thing is that once we’ve done whole genome sequencing and start to unravel more then we can put more genes into the panels and offer more treatments to patients. I’ve been working on a particular case study at the moment. This is in a lung cancer patient that presented with a left lower nodule in the lung.
Skip to 3 minutes and 51 seconds We offered the patient a panel test and looked at a number of genes including the NRAS, the KRAS, the PIK3CA genes, as well as the EGFR gene, and looked at ALK rearrangements. This patient then turned out to have an EGFR-sensitising variant. This was a frameshift variant, causing a truncated or shortened protein. It’s been known that these patients will respond to EGFR-inhibitor therapies So we have an answer for this patient that we can now offer a treatment for. We’re hoping, through whole genome sequencing, to be able to find answers for more patients and to be able to look for more genes to add to our panels
Skip to 4 minutes and 35 seconds and to be able to find more therapies for the future so we can help more patients.
Patient stories: when whole genome sequencing provides answers
In this video you will hear about three specific cases and areas of medicine where genome sequencing has helped patients.
Dr Nick Loman explains how whole genome sequencing was used to track down the source of an outbreak of salmonella; Professor Maria Bitner-Glindzicz picks up the story of Jessica Wright, who we met earlier in the course, to tell us about the diagnosis Jessica received thanks to whole genome sequencing as a participant in the 100,000 Genomes Project; and Samantha Butler talks about the use of genetic testing to target cancer treatment and the potential for whole genome sequencing in the field of cancer.
We learn a number of interesting facts.
Whole genome sequencing was recently used to investigate and bring to a close a hospital outbreak of salmonella in Birmingham.
Whole genome sequencing gives the whole picture, making it possible to detect even a single mutation in the five million bases that make up the salmonella genome; and this can be enough to determine whether an individual case is part of a larger outbreak or not – in other words, whether individual cases are related to one another.
Whole genome sequencing was used to link later outbreaks across Europe, and to track the source of the outbreak – three chicken farms in Germany which were later closed down.
There are large numbers of people with undiagnosed rare diseases that clinicians suspect are genetic but where the exact gene or genes responsible are not known.
Whole genome sequencing makes it possible to analyse all of an individual’s genetic material to try and find the cause of a particular condition.
In the case of Jessica Wright, who we met earlier in the course, blood samples were taken from her and her parents, and the results from sequencing enabled scientists to identify one small change in one of Jessica’s genes that was not present in either parent.
Scientists confirmed that the gene that does not function correctly in Jessica is responsible for making a protein that allows glucose to be transported to the brain from the blood, and this gene variant was identified as the cause of her epilepsy.
Scientists and doctors know that this type of epilepsy can be controlled by changing to a ketogenic diet, which uses ketones as an alternative source of energy; thus, Jessica was able to switch to the ketogenic diet and her medication was scaled down.
Whole genome sequencing is being used more in the area of research than in diagnostics in cancer; this is because, currently, targeted panel screening can achieve the same results as whole genome sequencing, and it is cheaper and faster.
It is hoped that whole genome sequencing will enable scientists to identify more genes that are associated with cancer so that these can be added to the panels of genes that are currently tested.
In some cancer cases, the results from genetic testing enable scientists to make decisions regarding treatment and management that will benefit individual patients.
As an example of a case where genetic testing guides treatment, Samantha Butler discusses a panel test for lung cancer, where, if a specific variation in the EGFR gene is detected, clinicians can offer specific EGFR inhibitor therapies that are known to be beneficial for particular patients.
Research from whole genome sequencing, as well as identifying new genes associated with cancer, could also mean that scientists are able to develop more targeted treatments and therapies.
Here you can see that while there is still progress to be made in our understanding of the genome, patients and clinicians are already seeing real benefits from the advances in technology and science that have been made.