--- title: How VarSome Clinical powered Gencell to become Colombia’s first CAP-accredited molecular genetics lab description: We speak with Marcela Gálvez, MD, MSc (Medical and Scientific Director, Gencell LATAM) about how VarSome Clinical powered Gencell to achieve CAP accreditation. image: https://news.varsome.com/hubfs/VarSome%20Picks%20Blog.png --- [![VarSome](https://news.varsome.com/hubfs/VarSome_February2020%20Theme/Images/logo.png)](https://varsome.com/) - Editions - [More about VarSome.com](https://varsome.com/varsome-editions/varsome/) - [More about VarSome Premium](https://varsome.com/varsome-editions/varsome-premium/) - [More about VarSome Clinical](https://varsome.com/varsome-editions/varsome-clinical/) - [Learn more about APIs](https://varsome.com/information/varsome-api-info/) - About - Resources - [Library](https://varsome.com/library/) - [Documentation](https://docs.varsome.com/) - [Query types](https://varsome.com/about/examples/) - [IVDR](https://landing.varsome.com/ivdr-whitepaper) - [Germline Classification](https://varsome.com/about/resources/acmg-implementation/) - [Somatic Classification](https://varsome.com/about/resources/amp-implementation/) - Partners - [Distributors](https://varsome.com/distributors/) - [Partners](https://varsome.com/partners/) - [Become a partner](https://landing.varsome.com/become-varsome-partner) - General - [The Company](https://saphetor.com/about/) - [Cite VarSome](https://varsome.com/about/varsome-citations/) - [Link to VarSome](https://varsome.com/how-do-i-create-link-varsome/) - [Contact](https://landing.varsome.com/contact) - [Community](https://varsome.com/community-contributions/) - [Blog](https://blog.varsome.com/) [Community](https://news.varsome.com/en/tag/community) [VarSome.com](https://news.varsome.com/en/tag/varsome-com) [VarSome Clinical](https://news.varsome.com/en/tag/varsome-clinical) # How VarSome Clinical powered Gencell to become Colombia’s first CAP-accredited molecular genetics lab By [Lyndsey Fletcher](https://news.varsome.com/en/author/lyndsey-fletcher) on October, 15 2026 ### Categories - Select a Topic - [All](https://news.varsome.com/en) - [Partnerships](https://news.varsome.com/en/tag/partnerships) - [News](https://news.varsome.com/en/tag/news) - [Press Releases](https://news.varsome.com/en/tag/press-releases) - [VarSome Clinical](https://news.varsome.com/en/tag/varsome-clinical) - [Community](https://news.varsome.com/en/tag/community) - [Platform Updates](https://news.varsome.com/en/tag/platform-updates) - [VarSome.com](https://news.varsome.com/en/tag/varsome-com) - [Events](https://news.varsome.com/en/tag/events) - [Oncology](https://news.varsome.com/en/tag/oncology) - [Technology](https://news.varsome.com/en/tag/technology) - [VarSome.com Premium](https://news.varsome.com/en/tag/varsome-com-premium) - [Conferences](https://news.varsome.com/en/tag/conferences) - [Germline](https://news.varsome.com/en/tag/germline) - [VarSome in Action](https://news.varsome.com/en/tag/varsome-in-action) - [VarSome Team](https://news.varsome.com/en/tag/varsome-team) - [Awareness Days](https://news.varsome.com/en/tag/awareness-days) - [Whitepaper](https://news.varsome.com/en/tag/whitepaper) - [ACMG](https://news.varsome.com/en/tag/acmg) - [KnowledgeHub](https://news.varsome.com/en/tag/knowledgehub) - [Research Brief](https://news.varsome.com/en/tag/research-brief) - [VarSome API](https://news.varsome.com/en/tag/varsome-api) - [Application Note](https://news.varsome.com/en/tag/application-note) - [Community Q&A](https://news.varsome.com/en/tag/community-qa) - [VarSome Insights](https://news.varsome.com/en/tag/varsome-insights) ### Stay up to date ##### Search The Blog [Back to main Blog](https://news.varsome.com/en) [![](https://news.varsome.com/hs-fs/hubfs/1780856576699.png?height=100&name=1780856576699.png)](https://news.varsome.com/en/author/lyndsey-fletcher#blog-listing-section) ###### [Lyndsey Fletcher](https://news.varsome.com/en/author/lyndsey-fletcher#blog-listing-section) Content Marketer In a historic milestone for Latin American healthcare, our partner Gencell LATAM has officially become the **first diagnostic laboratory in Colombia to achieve prestigious CAP (College of American Pathologists) accreditation** in molecular biology and genetics. This benchmark recognition underscores Gencell’s relentless dedication to delivering world-class analytical quality, empowering physicians, health insurers, and patients across the region with clinical results backed by the highest international standards. This achievement also marks a major highlight for VarSome: Gencell is the first CAP-accredited laboratory in Latin America to integrate **VarSome Clinical** into its routine diagnostic workflow. Serving as the bioinformatic backbone for Gencell's whole exome sequencing (WES) validation, VarSome Clinical provided the end-to-end analytical precision, security, and traceability required to pass CAP’s rigorous inspection. We spoke with Marcela Gálvez, MD, MSc (Medical and Scientific Director, Gencell LATAM), to discuss how this breakthrough positions Gencell as a regional reference center and how VarSome Clinical supports their standard of excellence. ## **The milestone** “We are the first diagnostic laboratory in Colombia accredited by CAP in molecular biology and genetics,” says Marcela. “Although the validation focused on our whole exome sequencing assay, the accreditation covers the laboratory as a whole: our quality system, our people, and our processes. We expect it to strengthen the trust of the physicians who order our tests, to give our patients, partners and customers assurance of international-level quality, to support our work with health insurers and healthcare institutions, and to consolidate Gencell as a regional reference center for genomic diagnosis in Latin America.” By pursuing CAP accreditation, Gencell set out to demonstrate that its diagnostic testing meets globally recognized benchmarks rather than just regional standards, giving healthcare providers absolute confidence in every report generated. “The process and the accreditation itself have strengthened an increasingly demanding culture of commitment to quality across all our teams, and a deeper commitment to documenting every process, from sample reception to the final report. For our clients, this translates into results that are traceable, reproducible, and defensible to international standards.” ## **The challenge** Validating a whole exome sequencing (WES) assay covering single nucleotide variants (SNVs), insertions/deletions (indels), and copy number variants (CNVs) requires extreme bioinformatic accuracy and performance across complex genomic regions. “The hardest part was designing a study that covered the full workflow, from DNA extraction to bioinformatic analysis and interpretation, while keeping it practical to run. The validation even included cases in technically difficult regions,” Marcela explains. “Homopolymeric regions and genes with highly homologous pseudogenes remain a known limitation of short-read sequencing, and being transparent about it was part of the work: in these regions, orthogonal confirmation with complementary methods is still required, and our workflow reflects that.” VarSome Clinical proved essential in overcoming these challenges. Implemented at Gencell since 2021, VarSome Clinical delivers an all-in-one platform processing raw sequencing data (FASTQ/BAM) into accurately annotated and classified variants. Leveraging **unmatched integration of over 150 public and proprietary genomic databases**, VarSome Clinical automates ACMG/AMP variant classification while maintaining complete transparency for clinical decision-making. Beyond that, two capabilities were especially relevant for Gencell. “First,” says Marcela, “version traceability: being able to document exactly which version of the pipeline and annotation sources produced each result is essential both for an audit and for clinical reproducibility. Second, CNV calling with visual plots, which helps our analysts and geneticists distinguish true CNVs from artifacts before deciding on orthogonal confirmation. In every case, the final classification remains under the review of our medical genetics team.” In addition, regulatory and quality assurance were equally important for a laboratory seeking CAP accreditation in Colombia. Certified as an **In Vitro Diagnostic (IVD) medical device under the European Union’s In Vitro Diagnostic Regulation (IVDR)** and registered with INVIMA in Colombia, VarSome Clinical operates within strict quality management frameworks including **ISO 13485** and **ISO 27001** for data security. This regulatory foundation ensured that Gencell’s bioinformatic workflow was treated by CAP inspectors as a fully validated diagnostic device operating under globally certified security and quality controls. This proved crucial during the CAP inspection; auditors meticulously evaluated the bioinformatic architecture, and VarSome Clinical's formal IVDR certification and ISO accreditations provided assurance regarding software stability and regulatory compliance. Furthermore, inspectors reviewed how Gencell’s analysts and geneticists are trained in the use of the software, and how that training and competency are documented and maintained over time. ## **Working with VarSome Clinical** Gencell designed a comprehensive validation scheme evaluating intra-run and inter-run repeatability, library prep systems, and multiple short-read sequencing platforms, using both clinical samples and GIAB/NA12878 reference materials to establish true Limits of Detection (LOD). “We considered this design right for CAP because it challenges every step that can introduce variability, from library preparation to sequencing and bioinformatic analysis, and because it reflects exactly how we work in clinical practice,” Marcela states. During the protocol review, VarSome's team raised how the reference sample was diluted; diluting with water or buffer only reduces total DNA input and depth, not the real allele fraction, so the nominal percentage would not reflect true VAF. Using a wild-type background gives a true LOD, and can be defended in an audit. Following this discussion, Gencell described and interpreted the LOD study accordingly. This aspect was defensible under scrutiny, resulting in zero observations from CAP inspectors. “When we reviewed the validation protocol together, the discussion about how to dilute the reference material for the limit of detection was a good example of how this collaboration works. It was a small technical detail, but it determined whether the LOD would truly reflect allele fraction and hold up under inspection. The Gencell team took it on board immediately, and that openness to scrutiny is what I've seen from them since we started working together in 2021,” stated Tomáš Kučera, PhD (Business Development Manager Iberoamérica, Saphetor/VarSome). “The experience \[working with the VarSome team\] was very positive,” says Marcela. “\[They\] reviewed our validation protocol in detail, gave technical recommendations and supported us throughout the process, including support and billing. That responsiveness helped us move forward efficiently and with confidence.” ## **Advice for other labs** Based on their experience, Gencell has some advice for other laboratories in the region that want to validate an NGS assay for CAP accreditation. - Define the scope clearly before starting, and cover the full workflow, not only the sequencing. - Include replicates across runs, instruments, and platforms to demonstrate reproducibility. - Have your protocol reviewed by someone outside your own team before running it. - Document deviations and keep full traceability of samples, reagents, and pipeline versions. - Be transparent about the limitations of the technique, such as homopolymeric regions or genes with pseudogenes, and define when orthogonal confirmation with complementary methods is required. ## **What’s next?** Gencell and VarSome continue to work together to ensure robust workflows and the best outcomes for patients. For Gencell, CAP accreditation is an ongoing commitment. “We will keep working under the highest quality standards to support the accurate diagnosis of genetic diseases across Latin America, and we are already preparing for CAP reaccreditation, which takes place every two years. We are convinced that our collaboration with VarSome will keep strengthening as we grow,” Marcela concludes. *“*I've worked alongside the Gencell team since 2021, and what has always stood out is their insistence on doing things properly, not just quickly,” concludes Tomáš. “This accreditation is the result of years of that discipline. Gencell is the first CAP-accredited laboratory in Latin America with VarSome Clinical as part of its diagnostic workflow, which makes this a milestone not only for Gencell but for us at VarSome as well. It shows that our platform can support a laboratory through one of the most demanding accreditations in laboratory medicine.”   *The College of American Pathologists (CAP) is a leading organization of board-certified pathologists and the world’s largest organization of its kind. CAP accreditation is internationally recognized as a benchmark for quality in laboratory medicine. Through a rigorous accreditation process, laboratories are assessed against comprehensive standards designed to ensure accuracy, consistency, and quality in testing, ultimately supporting better outcomes for patients and confidence for healthcare professionals.* *Gencell LATAM is Colombia's premier molecular genetics laboratory, providing high-complexity genomic testing services across Latin America. Partnered with VarSome since 2021, Gencell utilizes VarSome Clinical for high-throughput, CAP-accredited diagnostic analysis of clinical exomes and genomes.* [Previous Post](https://news.varsome.com/en/saphetor-appoints-gene-x-press-as-official-distributor-for-varsome-in-chile) ### Stay up to date ## Latest News [See all blog posts](https://blog.varsome.com) ![](https://news.varsome.com/hubfs/VarSome_February2020%20Theme/Images/logo.png) - VarSome Suite - [VarSome.com](https://saphetor.com/varsome-editions/varsome/) - [VarSome Premium](https://saphetor.com/varsome-editions/varsome-premium/) - [VarSome Clinical](https://saphetor.com/varsome-editions/varsome-clinical/) - [VarSome API](https://varsome.com/information/varsome-api-info/) - System Status - [System Status](http://status.saphetor.com/) - Resources - [Query Examples](https://varsome.com/about/examples/) - [Documentation](https://docs.varsome.com/) - [Help Center](https://docs.varsome.com/en) - [Cite VarSome](https://news.varsome.com/en/cite-varsome-the-human-genomic-variant-search-engine) - The Company - [About Saphetor SA](https://saphetor.com/about/) - [News](https://blog.varsome.com) - [Distributors](https://landing.varsome.com/distributors) - [Contact](https://saphetor.com/contact/) - Legal - [Terms of Use](https://varsome.com/terms/) - [Privacy Policy](https://varsome.com/privacy/) VarSome Suite is brought to you by [Saphetor SA](https://saphetor.com). © 2024 Saphetor SA – All Rights Reserved.