Name
Title | ||
|---|---|---|
Clinical knowledgebase to interprete genomic variations from targeted exome sequencing of patient tumor samples |
Abstract | ||
|---|---|---|
Targeted exome sequencing of patient tumor samples has been applied in a CLIA-certified molecular diagnostic lab to connect genetic variants to personalized treatments. The Jackson Laboratory has established a Cancer Treatment Profile (JAX-CTP) of 358 genes. We have also built a Clinical Knowledgebase (CKB) that enables annotation of genomic variations as predictive markers of cancer treatment responses, including drug sensitivity and resistance. Clinical trials on targeted cancer therapies in the United States and Canada are also integrated into the knowledgebase. In this report, we are presenting the integrated informatics framework, including the adoption of standard ontologies and transformation of genomic variations using Human Genome Variation Society (HGVS) nomenclature in our data loading process. Our framework uses regular expressions (regex) as control and is able to support a scalable number of variation and expression types in the molecular profiles, such as amino acid changes, gene amplifications and gene fusions. This process automatically maps genomic variants from the JAX clinical analytic pipeline to the predictive markers in the Clinical Knowledgebase. It enables our clinical analysis team to quickly interpret genomic variations in patient samples and identify clinically actionable variants with associated cancer treatment responses in the knowledgebase. This automation greatly improves the capacity to produce clinical reports by querying our CKB database. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1145/2808719.2811432 | BCB |
Field | DocType | Citations |
Informatics,Annotation,Gene,Biology,Clinical trial,Bioinformatics,Human genome,Exome sequencing,Cancer | Conference | 0 |
PageRank | References | Authors |
0.34 | 0 | 9 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Rangjiao Roger Liu | 1 | 0 | 0.34 |
| Anuradha Lakshminarayana | 2 | 0 | 0.34 |
| Daniel Durkin | 3 | 0 | 0.34 |
| Sara Patterson | 4 | 0 | 0.34 |
| Craig Hanna | 5 | 0 | 0.34 |
| Grace A. Stafford | 6 | 0 | 0.68 |
| Guruprasad Ananda | 7 | 0 | 0.34 |
| Krishna M. Karuturi | 8 | 0 | 0.34 |
| Susan M. Mockus | 9 | 0 | 0.34 |