Expanding the Clinical Utility of Targeted RNA Sequencing Panels beyond Gene Fusions to Complex, Intragenic Structural Rearrangements

SIMPLE SUMMARY: In blood cancers and solid tumors, genetic changes serve to initiate and promote cancer. These genetic changes can include rearrangements to genes which can alter gene function. Identification of gene rearrangements through molecular laboratory tests may help guide clinical care in patients with cancer. Different types of gene rearrangements can occur, including those within a gene and those between genes. Rearrangements occurring within a gene can be difficult to identify using current computational approaches. Our clinical laboratory designed sequencing panels for blood cancers and solid tumors to detect rearrangements within and between genes. In this study, we discuss our three-year experience using a laboratory method of targeted sequencing to detect gene rearrangements. We highlight our approach and the clinical utility for the reporting of rearrangements both within and between genes. ABSTRACT: Gene fusions are a form of structural rearrangement well established as driver events in pediatric and adult cancers. The identification of such events holds clinical significance in the refinement, prognostication, and provision of treatment in cancer. Structural rearrangements also extend beyond fusions to include intragenic rearrangements, such as internal tandem duplications (ITDs) or exon-level deletions. These intragenic events have been increasingly implicated as cancer-promoting events. However, the detection of intragenic rearrangements may be challenging to resolve bioinformatically with short-read sequencing technologies and therefore may not be routinely assessed in panel-based testing. Within an academic clinical laboratory, over three years, a total of 608 disease-involved samples (522 hematologic malignancy, 86 solid tumors) underwent clinical testing using Anchored Multiplex PCR (AMP)-based RNA sequencing. Hematologic malignancies were evaluated using a custom Pan-Heme 154 gene panel, while solid tumors were assessed using a custom Pan-Solid 115 gene panel. Gene fusions, ITDs, and intragenic deletions were assessed for diagnostic, prognostic, or therapeutic significance. When considering gene fusions alone, we report an overall diagnostic yield of 36% (37% hematologic malignancy, 41% solid tumors). When including intragenic structural rearrangements, the overall diagnostic yield increased to 48% (48% hematologic malignancy, 45% solid tumor). We demonstrate the clinical utility of reporting structural rearrangements, including gene fusions and intragenic structural rearrangements, using an AMP-based RNA sequencing panel.