Abstract
Precision genomic oncology—applying high throughput sequencing (HTS) at the point-of-care to inform clinical decisions—is a developing precision medicine paradigm that is seeing increasing adoption. Simultaneously, new developments in targeted agents and immunotherapy, when informed by rich genomic characterization, offer potential benefit to a growing subset of patients. Multiple previous studies have commented on methods for identifying both germline and somatic variants. However, interpreting individual variants remains a significant challenge, relying in large part on the integration of observed variants with biological knowledge. A number of data and software resources have been developed to assist in interpreting observed variants, determining their potential clinical actionability, and augmenting them with ancillary information that can inform clinical decisions and even generate new hypotheses for exploration in the laboratory. Here, we review available variant catalogs, variant and functional annotation software and tools, and databases of clinically actionable variants that can be used in an ad hoc approach with research samples or incorporated into a data platform for interpreting and formally reporting clinical results.
Highlights
Genomic technologies and approaches have transformed cancer research and have led to the production of large-scale cancer genomics compendia [1, 2]
The development of novel and effective targeted therapies has proceeded in parallel with and been accelerated by deeper, faster, and broader genomic characterization [6], enabling early application of molecular characterization at the point of care to inform clinical decision-making [7,8,9,10] and to address resistance to primary therapy [11]
Robust sequencing technologies and increasingly reliable bioinformatics pipelines, combined with parallel development of therapeutics and diagnostics has bolstered the field of precision genomic oncology
Summary
Genomic technologies and approaches have transformed cancer research and have led to the production of large-scale cancer genomics compendia [1, 2]. The resulting molecular characterization and categorization of individual samples from such compendia has driven development of molecular subtypes cancers as well as enhanced understanding of the molecular etiologies of carcinogenesis [3,4,5]. The development of novel and effective targeted therapies has proceeded in parallel with and been accelerated by deeper, faster, and broader genomic characterization [6], enabling early application of molecular characterization at the point of care to inform clinical decision-making [7,8,9,10] and to address resistance to primary therapy [11]. Genomic characterization has applications in immune approaches to cancer. Referred to as precision oncology [13], genomicsdriven oncology [14], genomic oncology, and even as precision medicine, the paradigm
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