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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 enterprise-wide, 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. FUNDING. This work was supported by DFCI, BWH, and the National Cancer Institute (5R33CA155554 and 5K23CA157631).

SUBMITTER: Sholl LM

PROVIDER: S-EPMC5111542 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Institutional implementation of clinical tumor profiling on an unselected cancer population.

Sholl Lynette M LM Do Khanh K Shivdasani Priyanka P Cerami Ethan E Dubuc Adrian M AM Kuo Frank C FC Garcia Elizabeth P EP Jia Yonghui Y Davineni Phani P Abo Ryan P RP Pugh Trevor J TJ van Hummelen Paul P Thorner Aaron R AR Ducar Matthew M Berger Alice H AH Nishino Mizuki M Janeway Katherine A KA Church Alanna A Harris Marian M Ritterhouse Lauren L LL Campbell Joshua D JD Rojas-Rudilla Vanesa V Ligon Azra H AH Ramkissoon Shakti S Cleary James M JM Matulonis Ursula U Oxnard Geoffrey R GR Chao Richard R Tassell Vanessa V Christensen James J Hahn William C WC Kantoff Philip W PW Kwiatkowski David J DJ Johnson Bruce E BE Meyerson Matthew M Garraway Levi A LA Shapiro Geoffrey I GI Rollins Barrett J BJ Lindeman Neal I NI MacConaill Laura E LE

JCI insight 20161117 19

<b>BACKGROUND.</b> Comprehensive genomic profiling of a patient's cancer can be used to diagnose, monitor, and recommend treatment. Clinical implementation of tumor profiling in an enterprise-wide, unselected cancer patient population has yet to be reported. <b>METHODS.</b> 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 ...[more]

PMID: 27882345

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Project description:IntroductionEmerging evidence has suggested that inherited factors are also involved in lung cancer development. However, most studies focused on well-elucidated cancer predisposition genes, the majority of which are tumor suppressor genes. The profile of germline mutations in oncogenic driver genes remains unrevealed, which might also provide potential clinical implications for lung cancer management.MethodsSequencing data from 36,813 unselected lung cancer patients who underwent somatic mutation profiling were retrospectively reviewed. All recruited patients had matched white blood cell samples sequenced in parallel using a capture-based panel including eight key lung cancer driver genes (epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), MET proto-oncogene, receptor tyrosine kinase (MET), Kirsten rat sarcoma viral oncogene homolog (KRAS), Erb-B2 receptor tyrosine kinase 2(ERBB2), ROS proto-oncogene 1, receptor tyrosine kinase (ROS1), ret proto-oncogene (RET), and B-Raf proto-oncogene, serine/threonine kinase (BRAF)). Likely pathogenic/pathogenic (LP/P) variants were called according to the classification criteria of the American College of Medical Genetics and Genomics. Variants of uncertain significance (VUS) located in the kinase domains of driver genes and occurring recurrently (n ≥3) were also included for further analyses.ResultsSeven different LP/P variants in EGFR, MET, or RET were identified in 0.03% of lung cancer patients (n = 14) and 25 different VUS in the kinase domains of seven driver genes (except KRAS) were found with a prevalence of 0.3% (n = 117).Collectively, germline mutations were most frequently seen in ROS1 (n = 31, 0.084%), followed by MET (n = 23, 0.062%), EGFR (n = 22, 0.06%), ALK (n = 22, 0.06%) and RET (n = 17, 0.046%). LP/P variants and VUS fell the most commonly in EGFR (n = 10, 72%) and ROS1 (n = 31, 26%), respectively. Of the 10 patients with EGFR LP/P germline mutation, 70% also acquired somatic EGFR driver mutation exon21 p.L858R or exon19 deletion at baseline; while the three patients with pathogenic germline RET mutation displayed distinct baseline somatic profiles of rare EGFR mutation or KRAS exon2 p.G12C. We discovered 11 germline mutations that also occurred somatically, including four LP/P variants and seven VUS.ConclusionWe present the first study to systemically characterize the germline mutation in oncogenic driver genes in a large cohort of unselected patients with lung cancers.

Project description:BackgroundEndotracheal tube (ETT) designs to decrease the risk of ventilator associated pneumonia (VAP) include supraglottic suctioning, and/or modifications of the cuff shape. The TaperGuard™ ETT has a tapered, polyvinylchloride cuff designed to reduce microaspiration around channels that form with a standard barrel-shaped cuff. We compared risk of postoperative pneumonia using the TaperGuard™ ETT and the standard ETT in surgical patients requiring general anesthesia with endotracheal intubation.MethodsWe used an interrupted time-series design to compare endotracheal intubation using the TaperGuard™ ETT (intervention cohort), and a historic cohort using the standard ETT (baseline cohort), among surgical patients requiring hospital admission. We compared the incidence of postoperative pneumonia in the intervention and baseline cohorts. Data were collected from the electronic health record and linked to patient-level data from National Surgical Quality Improvement Project. Additionally, we performed secondary analyses in a subgroup of patients at high risk of postoperative pneumonia.Results15,388 subjects were included; 6351 in the intervention cohort and 9037 in the baseline cohort. There was no significant difference in the incidence of postoperative pneumonia between the intervention cohort (1.62%) and the baseline cohort (1.79%). The unadjusted odds ratio (OR) of postoperative pneumonia was 0.90 (95% CI: 0.70, 1.16; p = 0.423) and the OR adjusted for patient characteristics and potential confounders was 0.90 (95% CI: 0.69, 1.19; p = 0.469), comparing the intervention and baseline cohorts. There was no a priori selected subgroup of patients for whom the use of the TaperGuard™ ETT was associated with decreased odds of postoperative pneumonia relative to the standard ETT. Hospital mortality was higher in the intervention cohort (1.5%) compared with the baseline cohort (1.0%; OR 1.46, 95% CI: 1.09, 1.95; p = 0.010).ConclusionsThe broad implementation of the use of the TaperGuard™ ETT for intubation of surgical patients was not associated with a reduction in the risk of postoperative pneumonia. In the setting of a low underlying postoperative pneumonia risk and the use of recommended preventative VAP bundles, further risk reduction may not be achievable by simply modifying the ETT cuff design in unselected or high-risk populations undergoing inpatient surgery.Trial registrationClinicalTrials.gov, ID NCT02450929 .

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Institutional implementation of clinical tumor profiling on an unselected cancer population.

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Institutional implementation of clinical tumor profiling on an unselected cancer population.

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