title: Mutation based treatment recommendations from next generation sequencing data: a comparison of web tools.
abstract: Interpretation of complex cancer genome data, generated by tumor target profiling platforms, is key for the success of personalized cancer therapy. How to draw therapeutic conclusions from tumor profiling results is not standardized and may vary among commercial and academically-affiliated recommendation tools. We performed targeted sequencing of 315 genes from 75 metastatic breast cancer biopsies using the FoundationOne assay. Results were run through 4 different web tools including the Drug-Gene Interaction Database (DGidb), My Cancer Genome (MCG), Personalized Cancer Therapy (PCT), and cBioPortal, for drug and clinical trial recommendations. These recommendations were compared amongst each other and to those provided by FoundationOne. The identification of a gene as targetable varied across the different recommendation sources. Only 33% of cases had 4 or more sources recommend the same drug for at least one of the usually several altered genes found in tumor biopsies. These results indicate further development and standardization of broadly applicable software tools that assist in our therapeutic interpretation of genomic data is needed. Existing algorithms for data acquisition, integration and interpretation will likely need to incorporate artificial intelligence tools to improve both content and real-time status.
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Jaymin M
authors.initials: JM
authors.lastname: Patel
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Knopf
authors.affiliation: Radiology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Reiner
authors.affiliation: Pathology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Veerle
authors.initials: V
authors.lastname: Bossuyt
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Lianne
authors.initials: L
authors.lastname: Epstein
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: DiGiovanna
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Gina
authors.initials: G
authors.lastname: Chung
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Silber
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Tara
authors.initials: T
authors.lastname: Sanft
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Hofstatter
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mougalian
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Maysa
authors.initials: M
authors.lastname: Abu-Khalaf
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: James
authors.initials: J
authors.lastname: Platt
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Shi
authors.affiliation: Pathology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Gershkovich
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Christos
authors.initials: C
authors.lastname: Hatzis
authors.affiliation: Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
authors.forename: Lajos
authors.initials: L
authors.lastname: Pusztai
mesh_terms: D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D004360:Drug Therapy, Computer-Assisted / Q000379:methods* / Q000592:standards*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D058990:Molecular Targeted Therapy; D057285:Precision Medicine / Q000379:methods / Q000592:standards; D012984:Software
keywords: biomarkers and intervention studies; breast cancer; mutation based treatment recommendations; personalized medicine; tumor profiling