Institutional implementation of clinical tumor profiling on an unselected cancer population

Abstract

BACKGROUND.Comprehensive genomic profiling of a patient's cancer can be used to diagnose, monitor, and recommend treatment. Clinical implementation of tumor profiling in an enterprisewide, unselected cancer patient population has yet to be reported. METHODS.We deployed a hybrid-capture and massively parallel sequencing assay (OncoPanel) for all adult and pediatric patients at our combined cancer centers. Results were categorized by pathologists based on actionability. We report the results for the first 3,727 patients tested.RESULTS. Our cohort consists of cancer patients unrestricted by disease site or stage. Across all consented patients, half had sufficient and available (>20% tumor) material for profiling; once specimens were received in the laboratory for pathology review, 73% were scored as adequate for genomic testing. When sufficient DNA was obtained, OncoPanel yielded a result in 96% of cases. 73% of patients harbored an actionable or informative alteration; only 19% of these represented a current standard of care for therapeutic stratification. The findings recapitulate those of previous studies of common cancers but also identify alterations, including in AXL and EGFR, associated with response to targeted therapies. In rare cancers, potentially actionable alterations suggest the utility of a "cancer-agnostic" approach in genomic profiling. Retrospective analyses uncovered contextual genomic features that may inform therapeutic response and examples where diagnoses revised by genomic profiling markedly changed clinical management. CONCLUSIONS.Broad sequencing-based testing deployed across an unselected cancer cohort is feasible. Genomic results may alter management in diverse scenarios; however, additional barriers must be overcome to enable precision cancer medicine on a large scale.

Oral keratosis of unknown significance shares genomic overlap with oral dysplasia

“…Libraries were pooled in equal volume and sequenced on an Illumina MiSeq Nano flow cell to estimate concentration based on the number of index reads per sample (all samples yielded ≥250 ng DNA to pursue hybrid capture). Library hybridization used a custom biotinylated RNA bait set (Agilent SureSelect) targeting the full coding regions of 447 genes and 60 intronic regions (OncoPanel version 3; Garcia et al, ; Sholl et al, ; Appendix ). Hybrid‐capture libraries were then sequenced on an Illumina HiSeq 3,000.…”

Clinicopathologic and genetic characteristics of young patients with pleural diffuse malignant mesothelioma

“…The OncoPanel targeted hybrid-capture-based next generation sequencing assay was performed at Brigham and Women’s Hospital after DNA isolation from formalin-fixed paraffin-embedded tissue sections containing more than 20% tumor using a solution-phase Agilent SureSelect hybrid capture kit and Illumina HiSeq 2500 sequencer as previously described. 17 Massively parallel sequencing was used to survey exonic DNA sequences from 275 cancer-related genes including CDKN2A, NF2 , and BAP1 , and 113 intronic sequences from 30 genes, including BAP1 , to detect large deletions and gene rearrangements. Sample reads were analyzed and interpreted using a custom pipeline, including mutation calls generated using MuTect 18 and GATK, copy number calls using VisCap Cancer, 19 and structural variants using BreakMer.…”

Clinical and mutational spectrum of highly differentiated, paired box 3:forkhead box protein o1 fusion–negative rhabdomyosarcoma: A report from the Children's Oncology Group

“…Samples were prepared for sequencing as previously described 16 . Briefly, prior to library preparation, DNA was fragmented (Covaris sonication) to 250 bp and further purified using Agentcourt AMPure XP beads.…”