2 - Development of a Clinical Grade Interpretive Tool for Neoplastic Genomic Microarray Testing

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The identification of chromosomal abnormalities in solid tumor and hematologic malignancies is important for disease diagnosis, prognosis, progression, and therapeutic decision making. The recent application of a range of powerful molecular technologies including chromosomal microarray and next generation sequencing has dramatically increased the resolution of clinical genomic testing, leading to increased precision in the evaluation of the cancer genome. In the era of complex tumor genomics, a comprehensive and clinically-vetted knowledge base is critical to providing efficient, accurate and informative clinical interpretations. Although several public databases/resources are available, comprehensive clinical-grade resources directly facilitating interpretation and reporting of neoplastic microarray cases are still lacking. To achieve this goal, the Mayo Clinic Cytogenetics Laboratory is manually assembling and curating a comprehensive knowledge base of specific genes and genomic regions of clinical relevance, including a pan-cancer gene list and disease-specific gene lists for major groups of solid tumors and hematologic malignancies. Here we describe our processes, data sources, and annotation conventions. We also describe how we utilize Affymetrix Extensible Data (AED) files to visualize our curated gene lists alongside microarray findings, which facilitates scrutiny of relevant critical regions and rapid recognition of clinical significance. Using these newly created cancer interpretive tools we have built thus far, we have successfully provided efficient, accurate and informative interpretation of neoplastic microarray cases. We hope to share our experience with the CGC group and encourage community sharing of resources to facilitate best practices in neoplastic genomic microarray testing.