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New karyogram display improves Sapientia for clinical diagnosis

New karyogram display improves Sapientia for clinical diagnosis

7/29/2016    |    0 min read

Workflow and data visualisation features support whole exome sequencing

As the use of whole genome and exome analysis grows it is increasing the workload for the Genomic Medicine Centres. In response to requests for improved support for data visualisation and workflow, Congenica is launching a new version of its interpretation platform Sapientia™ ahead of the Association for Clinical Genetic Science (ACGS) and UK Genetic Testing Network (UKGTN) Exome Meeting on 29th July.

Sapientia is used by several of the presenters at the conference, and allows whole genome sequence data to be interpreted and the results presented within a clinically actionable diagnostic report.

Sapientia’s new data visualisation options include a new karyogram display that allows users to navigate chromosomes in a genome browser to see SNPs, small insertions and deletions, CNVs and larger structural variants in a single view.

To ease working with whole genome data – such as that from the Genomics England 100,000 Genomes Project – variant prioritisation tools have been incorporated, including the identification of potential disease-causing variants based on the patient’s phenotype.

New features of Sapientia also include elements to facilitate workflow such as enhancements to project structure to provide users with more granularity and the capacity for bulk upload through the new API. Further streamlining of the decision-making process improves the functionality for authorisation of clinical reports.

Simon C Ramsden of the Manchester Centre for Genomic Medicine (MCGM) will be talking at the ACGS/UKGTN Exome Meeting. MCGM has worked closely with Congenica to ensure Sapientia optimises genetic diagnosis.

MCGM is one of the early adopters of whole genome and exome analysis in a clinical setting and has found many benefits from this approach.

For example, in a case report in the Lancet[1] the MCGM team describes how a boy previously diagnosed as having non-syndromic infantile-onset retinal dystrophy (which causes visual impairment and ultimately blindness) had a sister who showed similar symptoms. Suspecting there may be a genetic mechanism, the boy was tested for 105 genes that had previously been implicated in retinal dystrophy. This test was unable to determine the genetic cause for the condition.

The group was able to investigate the whole exome (all the genes expressed in a human), and a genetic alteration was detected in a gene called IQCB1 which encodes nephrocystin, a protein vital for the function of both retinal photoreceptors and renal epithelia. This information suggested a much rarer cause of the retinal dystrophy, Senior-Loken syndrome, which may also give rise to kidney problems.

Further checks with the boy revealed that he was at risk of kidney failure. As a result, he has received timely and managed renal transplantation. His sister is now also routinely monitored for signs of kidney failure.

Professor Graeme Black, director of MCGM, comments: “By using whole exome sequencing we were able to diagnose renal disease before acute presentation. We could identify an appropriate donor early, therefore reducing the time on dialysis.

“In a clinical setting whole exome sequencing has the power to accelerate diagnoses and to improve the development of personalised care pathways.”

Sapientia is validated by the NHS and Genomics England and is the interpretation platform used within the 100,000 Genomes Project.

The ACGS/UKGTN Exome Meeting is taking place on 29th July at Birmingham Women’s Hospital; find out more at https://www.bsgm.org.uk/events/.

[1] Pinpointing clinical diagnosis through whole exome sequencing to direct patient care; a case of Senior-Loken syndrome, Lancet Vol 385, May 9, 2015