Research

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16 pages, 512 KiB

Open AccessArticle

Real-World Evaluation of Universal Germline Screening for Cancer Treatment-Relevant Pharmacogenes

by Megan L. Hutchcraft, Nan Lin, Shulin Zhang, Catherine Sears, Kyle Zacholski, Elizabeth A. Belcher, Eric B. Durbin, John L. Villano, Michael J. Cavnar, Susanne M. Arnold, Frederick R. Ueland and Jill M. Kolesar

Cancers 2021, 13(18), 4524; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13184524 - 08 Sep 2021

Cited by 5 | Viewed by 2163

Abstract

The purpose of this study was to determine the frequency of clinically actionable treatment-relevant germline pharmacogenomic variants in patients with cancer and assess the real-world clinical utility of universal screening using whole-exome sequencing in this population. Cancer patients underwent research-grade germline whole-exome sequencing [...] Read more.

The purpose of this study was to determine the frequency of clinically actionable treatment-relevant germline pharmacogenomic variants in patients with cancer and assess the real-world clinical utility of universal screening using whole-exome sequencing in this population. Cancer patients underwent research-grade germline whole-exome sequencing as a component of sequencing for somatic variants. Analysis in a clinical bioinformatics pipeline identified clinically actionable pharmacogenomic variants. Clinical Pharmacogenetics Implementation Consortium guidelines defined clinical actionability. We assessed clinical utility by reviewing electronic health records to determine the frequency of patients receiving pharmacogenomically actionable anti-cancer agents and associated outcomes. This observational study evaluated 291 patients with cancer. More than 90% carried any clinically relevant pharmacogenetic variant. At least one disease-relevant variant impacting anti-cancer agents was identified in 26.5% (77/291). Nine patients with toxicity-associated pharmacogenomic variants were treated with a relevant medication: seven UGT1A1 intermediate metabolizers were treated with irinotecan, one intermediate DPYD metabolizer was treated with 5-fluorouracil, and one TPMT poor metabolizer was treated with mercaptopurine. These individuals were more likely to experience treatment-associated toxicities than their wild-type counterparts (p = 0.0567). One UGT1A1 heterozygote died after a single dose of irinotecan due to irinotecan-related adverse effects. Identifying germline pharmacogenomic variants was feasible using whole-exome sequencing. Actionable pharmacogenetic variants are common and relevant to patients undergoing cancer treatment. Universal pharmacogenomic screening can be performed using whole-exome sequencing data originally obtained for quality control purposes and could be considered for patients who are candidates for irinotecan, 5-fluorouracil, capecitabine, and mercaptopurine. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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11 pages, 231 KiB

Open AccessArticle

Potential Utility of Pre-Emptive Germline Pharmacogenetics in Breast Cancer

by Philip S. Bernard, Whitney Wooderchak-Donahue, Mei Wei, Steven M. Bray, Kevin C. Wood, Baiju Parikh and Gwendolyn A. McMillin

Cancers 2021, 13(6), 1219; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13061219 - 11 Mar 2021

Cited by 1 | Viewed by 3189

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

19 pages, 1714 KiB

Open AccessArticle

Genetic Predictors of Chemotherapy-Induced Peripheral Neuropathy from Paclitaxel, Carboplatin and Oxaliplatin: NCCTG/Alliance N08C1, N08CA and N08CB Study

by Araba A. Adjei, Camden L. Lopez, Daniel J. Schaid, Jeff A. Sloan, Jennifer G. Le-Rademacher, Charles L. Loprinzi, Aaron D. Norman, Janet E. Olson, Fergus J. Couch, Andreas S. Beutler, Celine M. Vachon and Kathryn J. Ruddy

Cancers 2021, 13(5), 1084; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13051084 - 03 Mar 2021

Cited by 11 | Viewed by 2771

Abstract

Chemotherapy-induced peripheral neuropathy (CIPN) is a common and potentially permanent adverse effect of chemotherapeutic agents including taxanes such as paclitaxel and platinum-based compounds such as oxaliplatin and carboplatin. Previous studies have suggested that genetics may impact the risk of CIPN. We conducted genome-wide [...] Read more.

Chemotherapy-induced peripheral neuropathy (CIPN) is a common and potentially permanent adverse effect of chemotherapeutic agents including taxanes such as paclitaxel and platinum-based compounds such as oxaliplatin and carboplatin. Previous studies have suggested that genetics may impact the risk of CIPN. We conducted genome-wide association studies (GWASs) for CIPN in two independent populations who had completed European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ)-CIPN20 assessments (a CIPN-specific 20-item questionnaire which includes three scales that evaluate sensory, autonomic, and motor symptoms). The study population N08Cx included 692 participants from three clinical trials (North Central Cancer Treatment Group (NCCTG) N08C1, N08CA, and N08CB) who had been treated with paclitaxel, paclitaxel plus carboplatin, or oxaliplatin. The primary endpoint for the GWAS was the change from pre-chemotherapy CIPN20 sensory score to the worse score over the following 18 weeks. Study population The Mayo Clinic Breast Disease Registry (MCBDR) consisted of 381 Mayo Clinic Breast Disease Registry enrollees who had been treated with taxane or platinum-based chemotherapy. The primary endpoint for the GWAS assessed was the earliest CIPN20 sensory score available after the completion of chemotherapy. In multivariate model analyses, chemotherapy regimen (p = 3.0 × 10⁻⁸) and genetic ancestry (p = 0.007) were significantly associated with CIPN in the N08Cx population. Only age (p = 0.0004) was significantly associated with CIPN in the MCBDR population. The SNP most associated with CIPN was rs56360211 near PDE6C (p =7.92 × 10⁻⁸) in N08Cx and rs113807868 near TMEM150C in the MCBDR (p = 1.27 × 10⁻⁸). Due to a lack of replication, we cannot conclude that we identified any genetic predictors of CIPN. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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15 pages, 1145 KiB

Open AccessArticle

Genetic Variations and Health-Related Quality of Life (HRQOL): A Genome-Wide Study Approach

by Araba A. Adjei, Camden L. Lopez, Daniel J. Schaid, Jeff A. Sloan, Jennifer G. Le-Rademacher, Charles L. Loprinzi, Aaron D. Norman, Janet E. Olson, Fergus J. Couch, Andreas S. Beutler, Celine M. Vachon and Kathryn J. Ruddy

Cancers 2021, 13(4), 716; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13040716 - 10 Feb 2021

Cited by 4 | Viewed by 2066

Abstract

Health-related quality of life (HRQOL) is an important prognostic patient-reported outcome in oncology. Because prior studies suggest that HRQOL is, in part, heritable, we performed a GWAS to elucidate genetic factors associated with HRQOL in breast cancer survivors. Physical and mental HRQOL were [...] Read more.

Health-related quality of life (HRQOL) is an important prognostic patient-reported outcome in oncology. Because prior studies suggest that HRQOL is, in part, heritable, we performed a GWAS to elucidate genetic factors associated with HRQOL in breast cancer survivors. Physical and mental HRQOL were measured via paper surveys that included the PROMIS-10 physical and mental health domain scales in 1442 breast cancer survivors participating in the Mayo Clinic Breast Disease Registry (MCBDR). In multivariable regression analyses, age and financial concerns were significantly associated with global physical health (age: p = 1.6 × 10⁻²³; financial concerns: p = 4.8 × 10⁻⁴⁰) and mental health (age: p = 3.5 × 10⁻⁷; financial concerns: p = 2.0 × 10⁻⁶⁹⁾. Chemotherapy was associated with worse global mental health (p = 0.01). In the GWAS, none of the SNPs reached the genome-wide association significance threshold of 5 × 10⁻⁸ for associations with either global physical or global mental health, however, a cluster of SNPs in SCN10A, particularly rs112718371, appeared to be linked to worse global physical health (p = 5.21 × 10⁻⁸). Additionally, SNPs in LMX1B, SGCD, PARP12 and SEMA5A were also moderately associated with worse physical and mental health (p < 10⁻⁶). These biologically plausible candidate SNPs warrant further study as possible predictors of HRQOL. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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20 pages, 482 KiB

Open AccessArticle

Pharmacogenetic Study of Trabectedin-Induced Severe Hepatotoxicity in Patients with Advanced Soft Tissue Sarcoma

by Maud Maillard, Christine Chevreau, Félicien Le Louedec, Manon Cassou, Caroline Delmas, Laure Gourdain, Jean-Yves Blay, Didier Cupissol, Emmanuelle Bompas, Antoine Italiano, Nicolas Isambert, Corinne Delcambre-Lair, Nicolas Penel, François Bertucci, Cécile Guillemet, Julien Plenecassagnes, Stéphanie Foulon, Étienne Chatelut, Axel Le Cesne and Fabienne Thomas

Cancers 2020, 12(12), 3647; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers12123647 - 04 Dec 2020

Cited by 2 | Viewed by 2167

Abstract

Hepatotoxicity is an important concern for nearly 40% of the patients treated with trabectedin for advanced soft tissue sarcoma (ASTS). The mechanisms underlying these liver damages have not yet been elucidated but they have been suggested to be related to the production of [...] Read more.

Hepatotoxicity is an important concern for nearly 40% of the patients treated with trabectedin for advanced soft tissue sarcoma (ASTS). The mechanisms underlying these liver damages have not yet been elucidated but they have been suggested to be related to the production of reactive metabolites. The aim of this pharmacogenetic study was to identify genetic variants of pharmacokinetic genes such as CYP450 and ABC drug transporters that could impair the trabectedin metabolism in hepatocytes. Sixty-three patients with ASTS from the TSAR clinical trial (NCT02672527) were genotyped by next-generation sequencing for 11 genes, and genotype–toxicity association analyses were performed with R package SNPassoc. Among the results, ABCC2 c.1249A allele (rs2273697) and ABCG2 intron variant c.-15994T (rs7699188) were associated with an increased risk of severe cytolysis, whereas ABCC2 c.3563A allele had a protective effect, as well as ABCB1 variants rs2032582 and rs1128503 (p-value < 0.05). Furthermore, CYP3A5*1 rs776746 (c.6986A > G) increased the risk of severe overall hepatotoxicity (p = 0.012, odds ratio (OR) = 5.75), suggesting the implication of metabolites in the hepatotoxicity. However, these results did not remain significant after multiple analysis correction. These findings need to be validated on larger cohorts of patients, with mechanistic studies potentially being able to validate the functional consequences of these variants. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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Review

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20 pages, 1154 KiB

Open AccessReview

Systematic Review of Pharmacogenetic Factors That Influence High-Dose Methotrexate Pharmacokinetics in Pediatric Malignancies

by Zachary L. Taylor, Jesper Vang, Elixabet Lopez-Lopez, Natanja Oosterom, Torben Mikkelsen and Laura B. Ramsey

Cancers 2021, 13(11), 2837; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13112837 - 07 Jun 2021

Cited by 26 | Viewed by 4597

Abstract

Methotrexate (MTX) is a mainstay therapeutic agent administered at high doses for the treatment of pediatric and adult malignancies, such as acute lymphoblastic leukemia, osteosarcoma, and lymphoma. Despite the vast evidence for clinical efficacy, high-dose MTX displays significant inter-individual pharmacokinetic variability. Delayed MTX [...] Read more.

Methotrexate (MTX) is a mainstay therapeutic agent administered at high doses for the treatment of pediatric and adult malignancies, such as acute lymphoblastic leukemia, osteosarcoma, and lymphoma. Despite the vast evidence for clinical efficacy, high-dose MTX displays significant inter-individual pharmacokinetic variability. Delayed MTX clearance can lead to prolonged, elevated exposure, causing increased risks for nephrotoxicity, mucositis, seizures, and neutropenia. Numerous pharmacogenetic studies have investigated the effects of several genes and polymorphisms on MTX clearance in an attempt to better understand the pharmacokinetic variability and improve patient outcomes. To date, several genes and polymorphisms that affect MTX clearance have been identified. However, evidence for select genes have conflicting results or lack the necessary replication and validation needed to confirm their effects on MTX clearance. Therefore, we performed a systematic review to identify and then summarize the pharmacogenetic factors that influence high-dose MTX pharmacokinetics in pediatric malignancies. Using the PRISMA guidelines, we analyzed 58 articles and 24 different genes that were associated with transporter pharmacology or the folate transport pathway. We conclude that there is only one gene that reliably demonstrates an effect on MTX pharmacokinetics: SLCO1B1. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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13 pages, 705 KiB

Open AccessReview

Germline Genetics of Prostate Cancer: Prevalence of Risk Variants and Clinical Implications for Disease Management

by David K. Doan, Keith T. Schmidt, Cindy H. Chau and William D. Figg

Cancers 2021, 13(9), 2154; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13092154 - 29 Apr 2021

Cited by 12 | Viewed by 4164

Abstract

Prostate cancer has entered into the era of precision medicine with the recent approvals of targeted therapeutics (olaparib and rucaparib). The presence of germline mutations has important hereditary cancer implications for patients with prostate cancer, and germline testing is increasingly important in cancer [...] Read more.

Prostate cancer has entered into the era of precision medicine with the recent approvals of targeted therapeutics (olaparib and rucaparib). The presence of germline mutations has important hereditary cancer implications for patients with prostate cancer, and germline testing is increasingly important in cancer screening, risk assessment, and the overall treatment and management of the disease. In this review, we discuss germline variants associated with inherited predisposition, prostate cancer risk and outcomes. We review recommendations for germline testing, available testing platforms, genetic counseling as well as discuss the therapeutic implications of germline variants relevant to prostate cancer treatments. Understanding the role of germline (heritable) mutations that affect prostate cancer biology and risk as well as the subsequent effect of these alterations on potential therapies is critical as the treatment paradigm shifts towards precision medicine. Furthermore, enhancing patient education tactics and healthcare system infrastructure is essential for the utilization of relevant predictive biomarkers and the improvement of clinical outcomes of patients with prostate cancer or at high risk of developing the disease. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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20 pages, 675 KiB

Open AccessReview

UGT1A1 Guided Cancer Therapy: Review of the Evidence and Considerations for Clinical Implementation

by Ryan S. Nelson, Nathan D. Seligson, Sal Bottiglieri, Estrella Carballido, Alex Del Cueto, Iman Imanirad, Richard Levine, Alexander S. Parker, Sandra M. Swain, Emma M. Tillman and J. Kevin Hicks

Cancers 2021, 13(7), 1566; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13071566 - 29 Mar 2021

Cited by 26 | Viewed by 6579

Abstract

Multi-gene assays often include UGT1A1 and, in certain instances, may report associated toxicity risks for irinotecan, belinostat, pazopanib, and nilotinib. However, guidance for incorporating UGT1A1 results into therapeutic decision-making is mostly lacking for these anticancer drugs. We summarized meta-analyses, genome-wide association studies, clinical [...] Read more.

Multi-gene assays often include UGT1A1 and, in certain instances, may report associated toxicity risks for irinotecan, belinostat, pazopanib, and nilotinib. However, guidance for incorporating UGT1A1 results into therapeutic decision-making is mostly lacking for these anticancer drugs. We summarized meta-analyses, genome-wide association studies, clinical trials, drug labels, and guidelines relating to the impact of UGT1A1 polymorphisms on irinotecan, belinostat, pazopanib, or nilotinib toxicities. For irinotecan, UGT1A1*28 was significantly associated with neutropenia and diarrhea, particularly with doses ≥ 180 mg/m², supporting the use of UGT1A1 to guide irinotecan prescribing. The drug label for belinostat recommends a reduced starting dose of 750 mg/m² for UGT1A1*28 homozygotes, though published studies supporting this recommendation are sparse. There was a correlation between UGT1A1 polymorphisms and pazopanib-induced hepatotoxicity, though further studies are needed to elucidate the role of UGT1A1-guided pazopanib dose adjustments. Limited studies have investigated the association between UGT1A1 polymorphisms and nilotinib-induced hepatotoxicity, with data currently insufficient for UGT1A1-guided nilotinib dose adjustments. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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15 pages, 987 KiB

Open AccessReview

Clinical CYP2D6 Genotyping to Personalize Adjuvant Tamoxifen Treatment in ER-Positive Breast Cancer Patients: Current Status of a Controversy

by Tessa A. M. Mulder, Mirjam de With, Marzia del Re, Romano Danesi, Ron H. J. Mathijssen and Ron H. N. van Schaik

Cancers 2021, 13(4), 771; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13040771 - 12 Feb 2021

Cited by 24 | Viewed by 7218

Abstract

Tamoxifen is a major option for adjuvant endocrine treatment in estrogen receptor (ER) positive breast cancer patients. The conversion of the prodrug tamoxifen into the most active metabolite endoxifen is mainly catalyzed by the enzyme cytochrome P450 2D6 (CYP2D6). Genetic variation in the [...] Read more.

Tamoxifen is a major option for adjuvant endocrine treatment in estrogen receptor (ER) positive breast cancer patients. The conversion of the prodrug tamoxifen into the most active metabolite endoxifen is mainly catalyzed by the enzyme cytochrome P450 2D6 (CYP2D6). Genetic variation in the CYP2D6 gene leads to altered enzyme activity, which influences endoxifen formation and thereby potentially therapy outcome. The association between genetically compromised CYP2D6 activity and low endoxifen plasma concentrations is generally accepted, and it was shown that tamoxifen dose increments in compromised patients resulted in higher endoxifen concentrations. However, the correlation between CYP2D6 genotype and clinical outcome is still under debate. This has led to genotype-based tamoxifen dosing recommendations by the Clinical Pharmacogenetic Implementation Consortium (CPIC) in 2018, whereas in 2019, the European Society of Medical Oncology (ESMO) discouraged the use of CYP2D6 genotyping in clinical practice for tamoxifen therapy. This paper describes the latest developments on CYP2D6 genotyping in relation to endoxifen plasma concentrations and tamoxifen-related clinical outcome. Therefore, we focused on Pharmacogenetic publications from 2018 (CPIC publication) to 2021 in order to shed a light on the current status of this debate. Full article

(This article belongs to the Special Issue Germline Pharmacogenetics of Cancer Treatment)

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