Please can you introduce yourself and share a bit about your role, institution, and the genetic services you provide?

I am a laboratory scientist working in the Molecular Diagnostics Laboratory at the National Children’s Hospital “Carlos Saenz-Herrera” in Costa Rica. Our laboratory serves as the national reference center for diagnosing genetic diseases in both children and adults. Additionally, we are part of the National Oncological Counseling Project, which has been operational since 2018. Within this project, we perform genetic analyses for adult participants across the country. I am part of the team responsible for conducting genetic tests, including whole exome sequencing and Sanger sequencing, as well as analyzing, interpreting, and reporting variants. Our laboratory collaborates closely with clinicians from various hospital specialties, holding monthly clinical meetings to discuss complex and challenging cases. This multidisciplinary approach helps improve diagnosis and patient management.

Which SOPHiA GENETICS applications do you currently use in your work?

Currently, we use the SOPHiA DDM™ Hereditary Cancer Solution v2.0, which includes 83 genes associated with hereditary cancer, and the SOPHiA DDM™ Whole Exome Solution. We rely on the SOPHiA DDM™ Platform for variant analysis.

What are the key benefits of using the SOPHiA DDM™ Platform in your lab?

Using the SOPHiA DDM™ Platform has significantly streamlined our workflow by reducing analysis time and optimizing variant interpretation. The platform provides easy access to multiple databases directly within its interface, which simplifies data contextualization.

One of the most valued features is the ability to build our own custom database. This functionality allows us to perform intra-sample comparisons (within the same run), inter-sample comparisons (across all runs over time), and inter-laboratory comparisons using SOPHiA DDM™'s tools. This is essential for validating findings and ensuring consistency in our analyses.

Having a custom database is particularly beneficial because public databases often lack adequate information about Latin American populations, especially Costa Rican populations. By maintaining our own database, we can track allele frequencies specific to our population and analyze potential founder effects or population-specific genetic behaviors. This capability not only facilitates trend analysis over time but also enhances our ability to identify patterns and anomalies in genetic data. Such insights are invaluable for developing more precise and personalized clinical strategies tailored to our population.

As part of our involvement in the National Oncological Counseling Project, we have analyzed approximately 1500 probands and 2300 relatives since 2018. Among these families, around 800 have hereditary breast/ovarian cancer syndrome. Notably, we observed that 43% of families diagnosed with breast/ovarian cancer have a pathogenic variant in BRCA2. Of these families with BRCA2 variants, 61% carry the c.9235delG variant.

This variant does not fall within regions typically associated with breast or ovarian cancer risk. Interestingly, it has also been identified in other types of cancer within Costa Rica, such as pancreatic and prostate cancer. These findings suggest a unique genetic architecture for breast and ovarian cancer in the Costa Rican population.

The discovery of this founder variant highlights the importance of understanding population-specific genetic markers to improve diagnostics.

How has your experience been working with the SOPHiA GENETICS team?

Our collaboration with SOPHiA GENETICS has been highly positive. The team is responsive and supportive, providing valuable guidance on how to maximize the platform’s functionalities for our specific needs.

Looking ahead, what excites you most about the future of genetic testing at National Children’s Hospital “Carlos Saenz-Herrera”?

Looking ahead, we are excited about the possibilities of integrating cutting-edge technologies into our laboratory workflows.

For instance:

- Optical Genome Mapping: This technology has enormous potential to revolutionize structural variant detection by providing high-resolution insights into chromosomal abnormalities.

- Somatic Sequencing: Expanding into somatic sequencing will enable us to analyze tumor-specific mutations more comprehensively.

These advancements will further enhance our ability to provide robust diagnostic solutions and personalized treatment strategies for patients across Costa Rica.

Elexandra Barboza-Arguedas and her team are a great example of how dedicated experts can combine technology and local knowledge to make a real difference. We’re proud to support their work as they continue to expand genetic testing in Costa Rica, uncovering insights that not only advance clinical insights today but help shape a more personalized, inclusive future for healthcare.

Click through to learn more about SOPHiA DDM™ exome and hereditary cancer solutions.