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Bernard PS, Wooderchak-Donahue W, Wei M, Bray SM, Wood KC, Parikh B, McMillin GA. Potential Utility of Pre-Emptive Germline Pharmacogenetics in Breast Cancer. Cancers (Basel) 2021; 13:cancers13061219. [PMID: 33799547 PMCID: PMC7998388 DOI: 10.3390/cancers13061219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/14/2022] Open
Abstract
Patients with breast cancer often receive many drugs to manage the cancer, side effects associated with cancer treatment, and co-morbidities (i.e., polypharmacy). Drug-drug and drug-gene interactions contribute to the risk of adverse events (AEs), which could lead to non-adherence and reduced efficacy. Here we investigated several well-characterized inherited (germline) pharmacogenetic (PGx) targets in 225 patients with breast cancer. All relevant clinical, pharmaceutical, and PGx diplotype data were aggregated into a single unifying informatics platform to enable an exploratory analysis of the cohort and to evaluate pharmacy ordering patterns. Of the drugs recorded, there were 38 for which high levels of evidence for clinical actionability with PGx was available from the US FDA and/or the Clinical Pharmacogenetics Implementation Consortium (CPIC). These data were associated with 10 pharmacogenes: DPYD, CYP2C9, CYP2C19, CYP2D6, CYP3A5, CYP4F2, G6PD, MT-RNR1, SLCO1B1, and VKORC1. All patients were taking at least one of the 38 drugs and had inherited at least one actionable PGx variant that would have informed prescribing decisions if this information had been available pre-emptively. The non-cancer drugs with PGx implications that were common (prescribed to at least one-third of patients) included anti-depressants, anti-infectives, non-steroidal anti-inflammatory drugs, opioids, and proton pump inhibitors. Based on these results, we conclude that pre-emptive PGx testing may benefit patients with breast cancer by informing drug and dose selection to maximize efficacy and minimize AEs.
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Affiliation(s)
- Philip S. Bernard
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA; (P.S.B.); (W.W.-D.)
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Whitney Wooderchak-Donahue
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA; (P.S.B.); (W.W.-D.)
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mei Wei
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
- Division of Oncology, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Steven M. Bray
- LifeOmic Inc., Indianapolis, IN 46202, USA; (S.M.B.); (K.C.W.); (B.P.)
| | - Kevin C. Wood
- LifeOmic Inc., Indianapolis, IN 46202, USA; (S.M.B.); (K.C.W.); (B.P.)
| | - Baiju Parikh
- LifeOmic Inc., Indianapolis, IN 46202, USA; (S.M.B.); (K.C.W.); (B.P.)
| | - Gwendolyn A. McMillin
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA; (P.S.B.); (W.W.-D.)
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
- Correspondence: ; Tel.: +1-801-583-2787 (ext. 2671)
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Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A. The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients. Mol Cancer Res 2019; 17:1075-1086. [PMID: 30651372 DOI: 10.1158/1541-7786.mcr-18-0996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/22/2018] [Accepted: 01/07/2019] [Indexed: 01/01/2023]
Abstract
Lower grade gliomas are invasive brain tumors that are difficult to completely resect neurosurgically. They often recur following resection and progress, resulting in death. Although previous studies have shown that specific germline variants increase the risk of tumor formation, no previous study has screened many germline variants to identify variants predictive of survival in patients with glioma. In this study, we present an approach to identify the small fraction of prognostic germline variants from the pool of over four million variants that we variant called in The Cancer Genome Atlas whole-exome sequencing and RNA sequencing datasets. We identified two germline variants that are predictive of poor patient outcomes by Cox regression, controlling for eleven covariates. rs61757955 is a germline variant found in the 3' UTR of GRB2 associated with increased KRAS signaling, CIC mutations, and 1p/19q codeletion. rs34988193 is a germline variant found in the tumor suppressor gene ANKDD1a that causes an amino acid change from lysine to glutamate. This variant was found to be predictive of poor prognosis in two independent lower grade glioma datasets and is predicted to be within the top 0.06% of deleterious mutations across the human genome. The wild-type residue is conserved in all 22 other species with a homologous protein. IMPLICATIONS: This is the first study presenting an approach to screening many germline variants to identify variants predictive of survival and our application of this methodology revealed the germline variants rs61757955 and rs34988193 as being predictive of survival in patients with lower grade glioma.
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Manjari Kiran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia.
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Wellmann R, Borden BA, Danahey K, Nanda R, Polite BN, Stadler WM, Ratain MJ, O'Donnell PH. Analyzing the clinical actionability of germline pharmacogenomic findings in oncology. Cancer 2018; 124:3052-3065. [PMID: 29742281 DOI: 10.1002/cncr.31382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 01/19/2023]
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 β1 [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 α1 [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.
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Affiliation(s)
- Rebecca Wellmann
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois
| | - Brittany A Borden
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois
| | - Keith Danahey
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Center for Research Informatics, The University of Chicago, Chicago, Illinois
| | - Rita Nanda
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Blase N Polite
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Walter M Stadler
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Mark J Ratain
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois.,Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois
| | - Peter H O'Donnell
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois.,Department of Medicine, The University of Chicago, Chicago, Illinois.,Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois
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Szucs TD, Szillat KP, Blozik E. Budget impact model for oncopharmacogenetics from the perspective of mandatory basic health insurance in Switzerland using the example of breast cancer. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2018; 11:67-69. [PMID: 29731658 PMCID: PMC5923251 DOI: 10.2147/pgpm.s154368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) can severely impact individual drug response and health outcomes in cancer patients. Genetic tests to screen for marker SNPs are available to adjust the drug dose of oncologicals to the patient's needs. However, it is unclear whether the positive effects outbalance the increased costs or even lead to an overall cost reduction. This very pragmatic analysis used three frequently used oncologicals for the treatment of breast cancer to evaluate whether preemptive pharmacogenetic testing may have a cost-reducing impact on health care spending in the Swiss health care system. Our results indicate that oncopharmacogenetics might help to reduce health care costs (ie, by avoiding adverse drug effects) and to increase efficiency of drugs in oncologic patients.
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Affiliation(s)
- Thomas D Szucs
- University of Basel, Institute of Pharmaceutical Medicine (ECPM), Basel, Switzerland
| | - Kevin P Szillat
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Eva Blozik
- Department of Health Sciences, Helsana Group, Zürich, Switzerland
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5
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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6
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Bocci G, Kerbel RS. Pharmacokinetics of metronomic chemotherapy: a neglected but crucial aspect. Nat Rev Clin Oncol 2016; 13:659-673. [DOI: 10.1038/nrclinonc.2016.64] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Offer SM, Diasio RB. Is It Finally Time for a Personalized Medicine Approach for Fluorouracil-Based Therapies? J Clin Oncol 2015; 34:205-7. [PMID: 26644533 DOI: 10.1200/jco.2015.64.2546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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8
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Zeron-Medina J, Ochoa de Olza M, Braña I, Rodon J. The Personalization of Therapy: Molecular Profiling Technologies and Their Application. Semin Oncol 2015; 42:775-87. [DOI: 10.1053/j.seminoncol.2015.09.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Pezzolo E, Modena Y, Corso B, Giusti P, Gusella M. Germ line polymorphisms as predictive markers for pre-surgical radiochemotherapy in locally advanced rectal cancer: a 5-year literature update and critical review. Eur J Clin Pharmacol 2015; 71:529-39. [PMID: 25740678 DOI: 10.1007/s00228-015-1824-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/11/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE Locally advanced rectal cancer is currently treated with pre-surgical radiotherapy and chemotherapy. Approximately one-half of patients obtain a relevant shrinkage/disappearance of tumour, with major clinical advantages. The remaining patients, in contrast, show no benefit and possibly need alternative treatment. To provide the best therapeutic option for each individual patient, predictive markers have been widely researched. This review was undertaken to evaluate recent progress made in this field. METHODS A systematic literature search was performed using PubMed and Scopus database, focused on germ line gene polymorphisms as biomarkers and response and toxicity as outcomes. Because an exhaustive previous review was available describing findings up to 2008, we restricted our analysis to the last 5 years. RESULTS Ten original research articles were found, reporting promising results for some candidate genes in drug metabolism (TYMS, MTHFR), DNA repair (XRCC1, OGG1, CCND1) and inflammation (SOD2, TGFB1)/immunity (IL13) pathways, but with no firm conclusion. All the studies had small sample size and were defined as exploratory. This review highlights pivotal molecular, clinical, genetic and statistical issues in the investigation of genetic polymorphisms as outcome predictors for rectal cancer and offers suggestions for future development. CONCLUSIONS What emerges is a clear need for new proposals, especially in view of the increasing evidence for tumour-host and gene-gene interactions during anticancer treatment, together with stronger adherence to proper methodological requirements.
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Affiliation(s)
- Elisa Pezzolo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Largo Meneghetti, 2, 35131, Padua, Italy,
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10
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Derks S, Diosdado B. Personalized cancer medicine: next steps in the genomic era. Cell Oncol (Dordr) 2015; 38:1-2. [PMID: 25720594 PMCID: PMC4359352 DOI: 10.1007/s13402-015-0221-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2015] [Indexed: 12/02/2022] Open
Affiliation(s)
- S. Derks
- />Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
- />VU University Medical Center, Amsterdam, The Netherlands
| | - B. Diosdado
- />Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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