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Curtis A, Yu Y, Carey M, Parfrey P, Yilmaz YE, Savas S. Examining SNP-SNP interactions and risk of clinical outcomes in colorectal cancer using multifactor dimensionality reduction based methods. Front Genet 2022; 13:902217. [PMID: 35991579 PMCID: PMC9385108 DOI: 10.3389/fgene.2022.902217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background: SNP interactions may explain the variable outcome risk among colorectal cancer patients. Examining SNP interactions is challenging, especially with large datasets. Multifactor Dimensionality Reduction (MDR)-based programs may address this problem.Objectives: 1) To compare two MDR-based programs for their utility; and 2) to apply these programs to sets of MMP and VEGF-family gene SNPs in order to examine their interactions in relation to colorectal cancer survival outcomes.Methods: This study applied two data reduction methods, Cox-MDR and GMDR 0.9, to study one to three way SNP interactions. Both programs were run using a 5-fold cross validation step and the top models were verified by permutation testing. Prognostic associations of the SNP interactions were verified using multivariable regression methods. Eight datasets, including SNPs from MMP family genes (n = 201) and seven sets of VEGF-family interaction networks (n = 1,517 SNPs) were examined.Results: ∼90 million potential interactions were examined. Analyses in the MMP and VEGF gene family datasets found several novel 1- to 3-way SNP interactions. These interactions were able to distinguish between the patients with different outcome risks (regression p-values 0.03–2.2E-09). The strongest association was detected for a 3-way interaction including CHRM3.rs665159_EPN1.rs6509955_PTGER3.rs1327460 variants.Conclusion: Our work demonstrates the utility of data reduction methods while identifying potential prognostic markers in colorectal cancer.
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Affiliation(s)
- Aaron Curtis
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yildiz E. Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John’s, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- *Correspondence: Sevtap Savas,
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Kiss KP, Varga G, Mikala G, Balassa K, Bors A, Kovy P, Meggyesi N, Kozma A, Csacsovszki O, Remenyi P, Valyi-Nagy I, Tordai A, Masszi T, Andrikovics H. The adverse effect of FOPNL genomic variant is reversed by bortezomib-based treatment protocols in multiple myeloma. Leuk Lymphoma 2017; 59:710-716. [PMID: 28691553 DOI: 10.1080/10428194.2017.1346250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Fibroblast growth factor receptor 1 oncogene partner N-terminal like gene (FOPNL) rs72773978 polymorphism was identified as an adverse prognostic factor in multiple myeloma (MM). We aimed to investigate the associations of rs72773978 with clinical characteristics and treatment outcome in 373 Hungarian MM patients. In our cohort, FOPNL polymorphism showed differential prognostic effect that depended on the treatment applied. Among patients treated with non-proteasome inhibitor (PI)-based therapy, carriership of the minor allele was significantly associated with adverse overall survival (p=.022). In contrast, the adverse effect was overcome by the application of PI-containing treatment (p=.048). Multivariate analyses revealed the independent adverse effect of rs72773978 on survival in the non-PI-treated group (p=.045), but not in PI treatment (OS: p=.093). We confirmed the adverse prognostic effect of rs72773978 associated with non-PI-based treatment regimens. Our results point to the importance of genotypic prognostic information associated with complex clinical background MM.
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Affiliation(s)
- Katalin Piroska Kiss
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Gergely Varga
- b 3rd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Gabor Mikala
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Katalin Balassa
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Andras Bors
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Petra Kovy
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Nora Meggyesi
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
| | - Andras Kozma
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Otto Csacsovszki
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Peter Remenyi
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Istvan Valyi-Nagy
- c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Attila Tordai
- d Department of Pathophysiology , Semmelweis University , Budapest , Hungary
| | - Tamas Masszi
- b 3rd Department of Internal Medicine , Semmelweis University , Budapest , Hungary.,c Department of Haematology and Stem Cell Transplantation , St. Istvan and St. Laszlo Hospital , Budapest , Hungary
| | - Hajnalka Andrikovics
- a Laboratory of Molecular Diagnostics , Hungarian National Blood Transfusion Service , Budapest , Hungary
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