“In just one clinic, ophthalmology, we used to offer a genetic test to about 10-15 per cent of patients. Now all of our patients are offered genetic testing because it’s more relevant to a far greater number of people.” Dr Simon Ramsden, lead geneticist for the Manchester Centre for Genomic Medicine (MCGM), described how he has embedded the genomic analysis platform Sapientia™ within clinical care in a presentation to the American Society of Human Genetics (ASHG) 20 October 2016.

Dr Ramsden heads the Laboratory Constitutional Genomics services at MCGM, where over 10,000 new patients each year are treated for a range of rare diseases including cancers, developmental disorders and disabilities such as hearing and vision loss. Manchester was the first NHS hospital to adopt Sapientia, which was developed by Congenica for genomic analysis and interpretation.

Sapientia equips clinicians with the tools to interpret mutations found in exomes and genomes and link them to the symptoms displayed by the patient. It provides a list of potential disease-causing variants that can be assigned pathogenicity by users.

Sapientia has allowed us to scale our operation to accommodate this explosion in genomic analysis. It offers us an opportunity to collate the information, do the analysis, and then make decisions within a single piece of software. It makes the whole system far more efficient.

Dr Simon Ramsden
Lead Geneticist for the Manchester Centre for Genomic Medicine

Whole exome analysis is now in routine practice at Manchester. In one case it has helped clinicians to predict renal disease in a patient who presented with retinal disease, and the patient had a successful kidney transplant as a result.

Dr Ramsden says the cost of genetic testing has come down dramatically, resulting in a ten-fold increase in tests since 2012. This has generated a huge amount of data that needs to be analysed. “Instead of sequencing one gene in a patient, we are looking at gene panels of 170,” he explains.

“Sapientia has allowed us to scale our operation to accommodate this explosion in genomic analysis. It offers us an opportunity to collate the information, do the analysis, and then make decisions within a single piece of software. It makes the whole system far more efficient.”

He gives the example of a baby with congenital cataracts: “In the past a baby with neurological problems would first see a paediatrician, then a neurologist, and if there’s ophthalmic problems they’ll see the ophthalmologist. Now on day one we can look at a panel of genes that cause cataracts and not worry about all the other biochemical tests that take a long time and cost the NHS a lot of money. It has radically changed the experience for patients.”

Supporting diagnosis

It’s not only ophthalmology where Sapientia is proving its worth: the same technology is used for metabolic disease and cardiac disease.

Dr Ramsden says: “A lot of pathologies are progressive, so when they first appear they’re not typical. It may be difficult for a clinician to make an accurate diagnosis until it has progressed to the full-blown disease. Whole exome analysis allows us to make that diagnosis much earlier.”

Dr Ramsden explains that the Human Genome Project has created a valuable resource by providing various methods of analysing variants. “What Sapientia does is give us a format: it is a web-based tool where we can take our data, compare it to what’s out there in the world, and support the clinicians to come up with a diagnosis.

“We now find ourselves in a multidisciplinary team (MDT) sitting in a room with surgeons, geneticists and scientists. The technology does not presume a particular diagnosis so we look at the genetics and the clinician comes to us with a range of symptoms, then we piece together a diagnosis. Sapientia has dramatically changed the way we operate.”