Oncopanel Assay

WHAT IS THE ONCOPANEL ASSAY?

The WiCell Oncopanel Assay is available as either a Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WES) assay, providing targeted analysis of 65 cancer-associated genes that may impact stem cell integrity. It is designed to identify pathogenic or likely pathogenic variants (inherited or acquired) that could compromise the genomic integrity of human pluripotent stem cells (hPSCs).

Genomic abnormalities in these genes can impact downstream differentiation, research reproducibility, and potential clinical applications. By assessing variants within a curated panel of high-priority oncogenes and tumor suppressors, the Oncopanel Assay provides insight into the genomic stability of hPSC lines, ensuring confidence in both research and translational use.

Variant interpretation of the targeted gene panel leverages expert-curated databases, computational prediction tools, peer-reviewed literature, and professional guidelines to classify sequence variants accurately and consistently.

Oncopanel Design

The 65-gene panel was designed to capture the most frequently mutated cancer driver genes associated with both differentiated target cell types and induced pluripotent stem cell (iPSC) donor cell types. Panel development incorporated data from publicly available cancer genomics resources and large-scale somatic mutation frequency studies (e.g., Mendiratta et al., 20211). In addition, genes known to acquire recurrent mutations during prolonged human pluripotent stem cell (hPSC) culture were included based on findings from Merkle et al. (2017) and Rouhani et al. (2022)2,3. This data-driven approach ensures coverage of mutations most relevant to stem cell research and clinical applications.

How it Works

Genomic DNA from submitted samples undergo WGS (up to 100x read depth) or WES (up to 200x read depth), which is performed by Genewiz (part of Azenta Life Sciences) using Illumina sequencing technology. WES provides a cost-effective alternative to WGS while maintaining high-quality coverage of coding regions.

Sequencing reads are aligned to the GRCh38 reference genome, and single nucleotide variants (SNVs) and small insertions/deletions (indels) are identified using validated analysis pipelines. Variant annotation and classification within the curated 65-gene panel are performed at WiCell using the QIAGEN Clinical Insight (QCI™) software tool.

Safeguard Your Stem Cell Research: Your Results

WiCell is committed to delivering accurate and reliable characterization services that safeguard your stem cell research.

Results for your cell line will be available within 30–35 business days from sample receipt. Upon completion of the assay, WiCell will provide an Oncopanel Variant Assessment Report summarizing the classification of variants within the curated 65-gene panel, along with raw sequencing data delivered on a physical hard drive.

Sample Types Accepted

• Live cultures
• Cryopreserved cells
• Frozen cell pellets
• Genomic DNA

Contact us with questions regarding sample submission, panel design, and more.

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