Tell us a bit about your laboratory.

The Genetics and Genomics Laboratory in which we operate belongs to a Local Health Authority in the Sardinia region. We provide molecular evaluation of gene alterations in many solid neoplasms to identify patients eligible for personalized treatments (i.e. targeted therapy). This service is provided to medical oncology departments in the city of Cagliari and many peripheral areas in the region.

What are the roots of your collaboration with SOPHiA GENETICS, and which application are you using?

The decision to collaborate with SOPHiA GENETICS was made in 2019, as our request to activate our NGS service was subject to CE-IVD certification of the library preparation and sequencing path. Furthermore, the process seemed quite linear to us.

We are currently using the SOPHiA DDM™ RNAtarget Oncology Solution (ROS) for RNA sequencing.

Can you describe your experience of using SOPHiA DDM™ ROS in routine for your RNA sequencing?

It has an excellent ability to identify fusion gene events involved in many oncological diseases. The application allowed us to identify several known and unknown molecular alterations (single nucleotide variants, Indels, gene fusion and exon skipping events) involved in various cancers, which represent biomarkers for approved and agnostic target drugs. In this way, it is possible to perform a combined analysis of different tumor pathologies in a single analysis session.

“It has an excellent ability to identify fusion gene events involved in many oncological diseases.”

Can you describe your experience with automating the workflow?

The automation of the workflow for library preparation has allowed us to standardize the quality (e.g. coverage of control genes, average size of transcripts, coverage of target regions).

In addition, we have solved the problem of complexity in library preparation. The three days of work required for preparation of libraries, up to the loading of the pools, have been reduced to only a few steps. The manual procedure now involves the set-up of the automation tool, loading of the pools into the sequencer, and approx. 2–3 days for the analysis of the data (for 16–24 samples).

“[With automation], we have solved the problem of complexity in library preparation. The three days of work required for preparation of libraries have been reduced to only a few steps.”

What are the greatest benefits of using SOPHiA DDM™ ROS?

The greatest benefit of this application is the advanced variant filtering capability and pathogenicity pre-classification that optimizes the data analysis flow and facilitates data interpretation.

In addition, the creation of a particularly exhaustive report for clinical information and ongoing trials relating to the pathologies under examination, make the results usable by the clinician for the therapeutic choice and prognosis of the disease.

We’d like to thank Manuela Badiali, Rita Congiu, and Stefania Murru for their time and for sharing their experience. Click here to learn more about SOPHiA DDM™ RNAtarget Technology and request a demo!

The Laboratory of Genetics and Genomics use a CE-IVD version of SOPHiA DDM™ ROS called SOPHiA DDM™ Dx ROS, available in in the European Economic Area (EEA), the United Kingdom and Switzerland. The CE-IVD application is not designed for use with automation – The Laboratory of Genetics and Genomics have validated the automated workflow for clinical use. SOPHiA GENETICS products are for Research Use Only, not for use in diagnostic procedures unless otherwise specified.