Sapientia genome analysis software by Congenica could cut costs and save lives

Whole genome analysis (WGA) enables rapid diagnosis of rare disease, ensuring that an appropriate course of management and treatment can be administered, possibly within days for acute neonatal cases, cutting the cost of intensive care and potentially saving lives. Rapid diagnosis is one of the many benefits of using the Sapientia™ genome analysis and interpretation platform that Dr Nick Lench, Chief Operating Officer of Congenica, will be discussing at Precision Medicine World Conference (PMWC) 2017 on January 23rd at 3.15pm.

“A significant advantage of whole genome analysis is that with a single genetic test you can screen for all disease-causing genetic mutations simultaneously,” says Dr Lench, co-founder of Congenica, a world-leading developer of genomics-based discovery and diagnostic technology.

“The traditional approach is to test for candidate genes first and then widen the scope. This is expensive and time-consuming, and for poorly babies in intensive care a delay in diagnosis may cause irreparable damage,” he continues. “The more genomes we analyse the better we become at interpretation, and ultimately this will benefit patients.”

Congenica has partnered with a number of hospitals to support the use of WGA for testing of babies that present with symptoms of rare genetic disease. Its Sapientia software scans the variants against its current database, and those known to be associated with disease are highlighted and linked to published literature and clinical observations. Novel mutations are annotated, analysed and a pathogenicity score assigned.

All the information is displayed graphically in a single web browser, making it easier for multi-disciplinary teams to understand and cross-reference with patient information, including symptoms and family medical history. This results in rapid diagnosis and an actionable clinical report within days of birth.

Congenica’s highly experienced team of clinical scientists is also providing interpretation services for Genomics England's 100,000 Genomes Project.

Over 500 reports have now been returned to Genomics England. By optimising the workflow in Sapientia, the team has managed to achieve a diagnostic yield of ~30%, with each case requiring an average of between 30-45 minutes for review.

Dr Lench continues: “We are learning all the time and fully expect to continue to reduce our review times significantly. With large enough datasets and the implementation of machine-learning approaches we can envisage a fully automated interpretation and reporting service for the vast majority of cases”.

Dr Lench explains that another benefit of whole genome sequencing is that the data can be stored and reanalysed when new information is available. Congenica’s experience suggests that the diagnostic yield will continue to increase as more patients are analysed.

“From our work on other large datasets, we have found that every year that you revisit the analysis, a further 5-10% of variants are picked up because more has been published,” explains Dr Lench. “However, it should be recognised that some causes are not detectable by existing next generation sequencing techniques.”