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Analyzing the clinical actionability of germline pharmacogenomic findings in oncology.

ABSTRACT: BACKGROUND:Germline and tumor pharmacogenomics impact drug responses, but germline markers less commonly guide oncology prescribing. The authors hypothesized that a critical number of clinically actionable germline pharmacogenomic associations exist, representing clinical implementation opportunities. METHODS:In total, 125 oncology drugs were analyzed for positive germline pharmacogenomic associations in journals with impact factors ?5. Studies were assessed for design and genotyping quality, clinically relevant outcomes, statistical rigor, and evidence of drug-gene effects. Associations from studies of high methodologic quality were deemed potentially clinically actionable, and translational summaries were written as point-of-care clinical decision support (CDS) tools and formally evaluated using the Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument. RESULTS:The authors identified germline pharmacogenomic results for 56 of 125 oncology drugs (45%) across 173 publications. Actionable associations were detected for 12 drugs, including 6 that had germline pharmacogenomic information within US Food and Drug Administration labels or published guidelines (capecitabine/fluorouracil/dihydropyrimidine dehydrogenase [DPYD], irinotecan/uridine diphosphate glucuronosyltransferase family 1 member A1 [UGT1A1], mercaptopurine/thioguanine/thiopurine S-methyltransferase [TPMT], tamoxifen/cytochrome P450 [CYP] family 2 subfamily D member 6 [CYP2D6]), and 6 others were novel (asparaginase/nuclear factor of activated T-cells 2 [NFATC2]/human leukocyte antigen D-related ?1 [HLA-DRB1], cisplatin/acylphosphatase 2 [ACYP2], doxorubicin/adenosine triphosphate-binding cassette subfamily C member 2/Rac family small guanosine triphosphatase 2/neutrophil cytosolic factor 4 [ABCC2/RAC2/NCF4], lapatinib/human leukocyte antigen DQ ?1 [HLA-DQA1], sunitinib/cytochrome P450 family 3 subfamily A member 5 [CYP3A5], vincristine/centrosomal protein 72 [CEP72]). By using AGREE II, the developed CDS summaries had high mean?±?standard deviation scores (maximum score, 100) for scope and purpose (92.7?±?5.1) and rigour of development (87.6?±?7.4) and moderate yet robust scores for clarity of presentation (58.6?±?25.1) and applicability (55.9?±?24.6). The overall mean guideline quality score was 5.2?±?1.0 (maximum score, 7). Germline pharmacogenomic CDS summaries for these 12 drugs were recommended for implementation. CONCLUSIONS:Several oncology drugs have actionable germline pharmacogenomic information, justifying their delivery through institutional pharmacogenomic implementations to determine clinical utility. Cancer 2018;124:3052-65. © 2018 American Cancer Society.

SUBMITTER: Wellmann R

PROVIDER: S-EPMC6354920 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Analyzing the clinical actionability of germline pharmacogenomic findings in oncology.

Wellmann Rebecca R Borden Brittany A BA Danahey Keith K Nanda Rita R Polite Blase N BN Stadler Walter M WM Ratain Mark J MJ O'Donnell Peter H PH

Cancer 20180509 14

<h4>Background</h4>Germline and tumor pharmacogenomics impact drug responses, but germline markers less commonly guide oncology prescribing. The authors hypothesized that a critical number of clinically actionable germline pharmacogenomic associations exist, representing clinical implementation opportunities.<h4>Methods</h4>In total, 125 oncology drugs were analyzed for positive germline pharmacogenomic associations in journals with impact factors ≥5. Studies were assessed for design and genotyp ...[more]

PMID: 29742281

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Project description:BackgroundIn order to establish the workflows required to implement a real-time process involving multi-omic analysis of patient samples to support precision-guided therapeutic intervention, a tissue acquisition and analysis trial was implemented. This report describes our findings to date, including the frequency with which mutational testing led to precision-guided therapy and outcome for those patients.MethodsEligible patients presenting to Oregon Health and Science University Knight Cancer Institute were enrolled on the study. Patients with biopsy proven metastatic or locally advanced unresectable prostate cancer, breast cancer, pancreatic adenocarcinoma, or refractory acute myelogenous leukemia receiving standard of care therapy were eligible. Metastatic site biopsies were collected and analyzed using the Knight Diagnostic Lab GeneTrails comprehensive solid tumor panel (124 genes). CLIA certified genomic information was made available to the treating physician.ResultsBetween 1/26/2017 and 5/30/2018, 38 patients were enrolled, with 28 successfully undergoing biopsy. Of these, 25 samples yielded sufficient tumor for analysis. The median biopsy cellularity and number of cores collected were 70% (15-90%) and 5 (2-20), respectively. No procedure-related complications occurred. GeneTrails analysis revealed that 22 of 25 (88%) tumor samples harbored at least one potentially actionable mutation, and 18 (72%) samples harbored 2 or more potentially actionable mutations. The most common genetic alterations identified involved: DNA damage repair genes, cell cycle regulating genes, PIK3CA/Akt/mTOR pathway, and FGF gene family. To date, CLIA certified genomic results were used by treating physicians for precision-guided therapy in 5 (23%) patients.ConclusionWe report the feasibility of real-time tissue acquisition and analysis to support a successful translational oncology platform. The workflow will provide the foundation to improve access and accrual to biomarker driven precision oncology trials.

Project description:Importance:The complete and timely dissemination of clinical trial data is essential to all fields of medicine, with delayed or incomplete data release having potentially deleterious effects on both patient care and scientific inquiry. While prior analyses have noted a substantial lag in the reporting of final clinical study results, we sought to refine these observations through use of a novel starting point for the measurement of dissemination delays: the date of a corporate press release regarding a phase 3 study's results. Objective:To measure the length of time elapsed between when a sponsor had results of study findings they deemed important to announce, and when the medical community had access to them. Design and Setting:Covering the years 2011 through 2016, we measured the delay from when 8 large pharmaceutical companies issued a press release announcing completed analyses of phase 3 clinical trials in oncology, and the public sharing of those results either on ClinicalTrials.gov or in a peer-reviewed biomedical journal as found via PubMed or Google Scholar. Press releases announcing regulatory steps and presentation schedules for conferences were excluded, as were those announcing results from preclinical trials, follow-up analyses, and studies of supportive care therapies or various modes of infusion for the same therapy. Main Outcomes and Measures:Time to public dissemination of clinical trial data. Results:Of the 100 press releases in our sample, 70 (70%) reported positive results, but only 31 (31%) included the magnitude of study findings. Through the end of follow-up, 99 (99%) of press releases had an associated peer-reviewed publication, complete data posting to ClinicalTrials.gov, or both, with a median time to reporting of 300 days (95% CI, 263-348 days). Positive findings were reported more quickly than negative ones (median of 272; 95% CI, 211-318 days vs 407; 95% CI, 298-705 days; log-rank P < .001). Conclusions and Relevance:Even for the most pressing study findings, median publication delays approach 1 year. As publication delays hinder research progress and advancements in clinical care, policies that enable early preprint release or public posting of completed data analysis should be pursued.

Project description:IntroductionWith the emergence of targeted therapies, there is a need to accurately identify more tumor biomarkers. The EXOMA trial was designed to offer tumor and germline exome sequencing (ES) to patients with solid malignant tumors and facing therapeutic failure. As hereditary cancer predispositions could be identified, with genetic counseling and health management implications, a genetic consultation was systematically established. This design needs to be discussed as genetic human resources are limited and indication of theranostic tests will increase.MethodsGenetic counseling was conducted within 15 days following inclusion in the study for patients recruited between December 2015 and July 2019. In silico analyses from theranostic ES were limited to 317 genes involved in oncogenesis, from both tumor and blood DNA.ResultsSix hundred and sixty six patients had a genetic consultation before ES. In 65/666 patients, 66 germline pathogenic or likely pathogenic (P/LP) variants were identified in 16 actionable genes and seven non-actionable genes according to French guidelines. 24/65 patients had previously received genetic analysis for diagnostic purposes, and for 17 of them, a P/LP variant had already been identified. Among the 48/65 remaining cases for which the EXOMA protocol revealed a previously unknown P/LP variant, only 19 met the criteria for genetic testing for inherited cancer risk after familial survey. These criteria had not been identified by the oncologist in 10 cases. In 21/65 cases, the variant was considered incidental.DiscussionIn 7.4% of patients, an undiagnosed hereditary genetic predisposition was identified, whether or not related to the clinical presentation, and germline analysis impacted oncological management for only 6.3% of the cohort. This low percentage should be weighed against the burden of systematic genetic consultation and urgent circuits. Information or training tools to form oncologists to the prescription of germline genetic analyses should be explored, as well as information supports and patient preferences.

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Analyzing the clinical actionability of germline pharmacogenomic findings in oncology.

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Analyzing the clinical actionability of germline pharmacogenomic findings in oncology.

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