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The 100 thousand genomes (100k) project

Regional Genomic Centres in the UK National Health Service have started an ambitious project to sequence 100,000 human genomes
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In Birmingham, we had a large outbreak of Salmonella enteritis in a local hospital and that’s very unusual. Salmonella is actually 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, it’s to really to understand what’s going on in the hospital. With genomes sequencing you get the 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 it is enough to be able to say whether something is part of an outbreak or not.
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The outbreak was controlled in the hospital and the problem went away. This same type then started to be detected in France, and in Germany, and in Europe, and so in fact, what we were able to do with the genome sequencing is trace back through the food distribution network to an actually, an individual producer of eggs in Germany, who actually maintained three chicken farms. And it’s the genetic information mapped beautifully onto the three chicken farms that was owned by this producer. There are a large number of people with undiagnosed genetic conditions and rare diseases in whom we suspect that the condition is genetic but we don’t actually know the gene responsible.
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The aim is to analyse all of an individual’s genetic material in order to try and find the cause of their rare disease. 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.
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And this is a particular type of epilepsy which occurs because the brain doesn’t get enough glucose from the diet, so the gene that’s not working in Jessica is responsible for making a protein that allows glucose to be transported into the brain from blood, and in Jessica’s case this doesn’t work properly. The importance of this diagnosis is that we know that this particular type of epilepsy responds very well to a ketogenic diet.
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So, 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, and as a result of this it means that Jessica’s anticonvulsant medication can be tailed down and the ketogenic diet can be introduced with what we hope will be a good effect. 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.
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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 have done the whole genome sequencing, and start to be able to unravel more, then we can start to put more genes into the panels ,and offer more treatments to patients. I’ve been working on a particular case study at the moment and this is in a lung cancer patient that presented with a left lower nodule in the lung.
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We offered the patient a panel test and looked at a number of genes including the NRAS, KRAS and PIK3CA genes, as well as the EGFR gene and looked at arc rearrangements. This patient then actually turned out to have an EGFR sensitising variant. This was a frameshift variant, causing a truncated or shortened protein. Now these patients will actually, or it’s been known that they will respond to EGFR inhibitor therapies. So we have an answer for this patient - that we can now offer them a treatment for.
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We’re hoping, through whole genome sequencing, to be able to find answers for more patients, to be able to look for more genes to add to our panels, and to be able to find more therapies for the future so we can actually help more patients.
Regional Genomic Centres in the UK National Health Service have started an ambitious project to sequence 100,000 human genomes. The 100K Genomes project has an educational division that produces information, infographics, and films that explain the technical and clinical aspects of the initiative.
In this video you will hear about three specific cases and areas of medicine where genome sequencing has helped patients.
Here is an infographic that explains some technical challenges for sequencing and analysing genomes.
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