title: The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies.
abstract: BACKGROUND
  Precision medicine in oncology relies on rapid associations between patient-specific variations and targeted therapeutic efficacy. Due to the advancement of genomic analysis, a vast literature characterizing cancer-associated molecular aberrations and relative therapeutic relevance has been published. However, data are not uniformly reported or readily available, and accessing relevant information in a clinically acceptable time-frame is a daunting proposition, hampering connections between patients and appropriate therapeutic options. One important therapeutic avenue for oncology patients is through clinical trials. Accordingly, a global view into the availability of targeted clinical trials would provide insight into strengths and weaknesses and potentially enable research focus. However, data regarding the landscape of clinical trials in oncology is not readily available, and as a result, a comprehensive understanding of clinical trial availability is difficult.
  
  
  RESULTS
  To support clinical decision-making, we have developed a data loader and mapper that connects sequence information from oncology patients to data stored in an in-house database, the JAX Clinical Knowledgebase (JAX-CKB), which can be queried readily to access comprehensive data for clinical reporting via customized reporting queries. JAX-CKB functions as a repository to house expertly curated clinically relevant data surrounding our 358-gene panel, the JAX Cancer Treatment Profile (JAX CTP), and supports annotation of functional significance of molecular variants. Through queries of data housed in JAX-CKB, we have analyzed the landscape of clinical trials relevant to our 358-gene targeted sequencing panel to evaluate strengths and weaknesses in current molecular targeting in oncology. Through this analysis, we have identified patient indications, molecular aberrations, and targeted therapy classes that have strong or weak representation in clinical trials.
  
  
  CONCLUSIONS
  Here, we describe the development and disseminate system methods for associating patient genomic sequence data with clinically relevant information, facilitating interpretation and providing a mechanism for informing therapeutic decision-making. Additionally, through customized queries, we have the capability to rapidly analyze the landscape of targeted therapies in clinical trials, enabling a unique view into current therapeutic availability in oncology.
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT, 06032, USA. sara.patterson@jax.org.
authors.forename: Sara E
authors.initials: SE
authors.lastname: Patterson
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT, 06032, USA. roger.liu@jax.org.
authors.forename: Rangjiao
authors.initials: R
authors.lastname: Liu
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT, 06032, USA. cara.statz@jax.org.
authors.forename: Cara M
authors.initials: CM
authors.lastname: Statz
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT, 06032, USA. daniel.durkin@jax.org.
authors.forename: Daniel
authors.initials: D
authors.lastname: Durkin
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT, 06032, USA. anuradha.lakshminarayana@jax.org.
authors.forename: Anuradha
authors.initials: A
authors.lastname: Lakshminarayana
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT, 06032, USA. susan.mockus@jax.org.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Mockus
mesh_terms: D000066491:Clinical Decision-Making; D002986:Clinical Trials as Topic; D023281:Genomics; D006801:Humans; D051188:Knowledge Bases; D058990:Molecular Targeted Therapy; D009154:Mutation / Q000235:genetics; D009363:Neoplasm Proteins / Q000235:genetics; D009369:Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D010361:Patients; D057285:Precision Medicine; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D009363:Neoplasm Proteins