DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf
Background Interactions among genetic variants are rarely studied but may explain a part of the variability in patient outcomes. Objectives In this study, we aimed to identify 1 to 3 way interactions among SNPs from five Wnt protein interaction networks that predict the 5-year recurrence risk in a c...
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Online Access: | https://doi.org/10.3389/fonc.2023.1122229.s001 https://figshare.com/articles/dataset/DataSheet_1_Multifactor_dimensionality_reduction_method_identifies_novel_SNP_interactions_in_the_WNT_protein_interaction_networks_that_are_associated_with_recurrence_risk_in_colorectal_cancer_pdf/22267630 |
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ftfrontimediafig:oai:figshare.com:article/22267630 2023-05-15T17:22:56+02:00 DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf Aaron A. Curtis Yajun Yu Megan Carey Patrick Parfrey Yildiz E. Yilmaz Sevtap Savas 2023-03-14T04:20:08Z https://doi.org/10.3389/fonc.2023.1122229.s001 https://figshare.com/articles/dataset/DataSheet_1_Multifactor_dimensionality_reduction_method_identifies_novel_SNP_interactions_in_the_WNT_protein_interaction_networks_that_are_associated_with_recurrence_risk_in_colorectal_cancer_pdf/22267630 unknown doi:10.3389/fonc.2023.1122229.s001 https://figshare.com/articles/dataset/DataSheet_1_Multifactor_dimensionality_reduction_method_identifies_novel_SNP_interactions_in_the_WNT_protein_interaction_networks_that_are_associated_with_recurrence_risk_in_colorectal_cancer_pdf/22267630 CC BY 4.0 Cancer Cancer Cell Biology Cancer Diagnosis Cancer Genetics Cancer Therapy (excl. Chemotherapy and Radiation Therapy) Chemotherapy Haematological Tumours Molecular Targets Radiation Therapy Solid Tumours Oncology and Carcinogenesis not elsewhere classified Wnt pathway recurrence multifactor dimensionality reduction SNP interactions colorectal cancer Dataset 2023 ftfrontimediafig https://doi.org/10.3389/fonc.2023.1122229.s001 2023-03-16T00:10:50Z Background Interactions among genetic variants are rarely studied but may explain a part of the variability in patient outcomes. Objectives In this study, we aimed to identify 1 to 3 way interactions among SNPs from five Wnt protein interaction networks that predict the 5-year recurrence risk in a cohort of stage I-III colorectal cancer patients. Methods 423 patients recruited to the Newfoundland Familial Colorectal Cancer Registry were included. Five Wnt family member proteins (Wnt1, Wnt2, Wnt5a, Wnt5b, and Wnt11) were selected. The BioGRID database was used to identify the proteins interacting with each of these proteins. Genotypes of the SNPs located in the interaction network genes were retrieved from a genome-wide SNP genotype data previously obtained in the patient cohort. The GMDR 0.9 program was utilized to examine 1-, 2-, and 3-SNP interactions using a 5-fold cross validation step. Top GMDR 0.9 models were assessed by permutation testing and, if significant, prognostic associations were verified by multivariable logistic regression models. Results GMDR 0.9 has identified novel 1, 2, and 3-way SNP interactions associated with 5-year recurrence risk in colorectal cancer. Nine of these interactions were multi loci interactions (2-way or 3-way). Identified interaction models were able to distinguish patients based on their 5-year recurrence-free status in multivariable regression models. The significance of interactions was the highest in the 3-SNP models. Several of the identified SNPs were eQTLs, indicating potential biological roles of the genes they were associated with in colorectal cancer recurrence. Conclusions We identified novel interacting genetic variants that associate with 5-year recurrence risk in colorectal cancer. A significant portion of the genes identified were previously linked to colorectal cancer pathogenesis or progression. These variants and genes are of interest for future functional and prognostic studies. Our results provide further evidence for the utility of GMDR models in ... Dataset Newfoundland Frontiers: Figshare |
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Open Polar |
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Frontiers: Figshare |
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ftfrontimediafig |
language |
unknown |
topic |
Cancer Cancer Cell Biology Cancer Diagnosis Cancer Genetics Cancer Therapy (excl. Chemotherapy and Radiation Therapy) Chemotherapy Haematological Tumours Molecular Targets Radiation Therapy Solid Tumours Oncology and Carcinogenesis not elsewhere classified Wnt pathway recurrence multifactor dimensionality reduction SNP interactions colorectal cancer |
spellingShingle |
Cancer Cancer Cell Biology Cancer Diagnosis Cancer Genetics Cancer Therapy (excl. Chemotherapy and Radiation Therapy) Chemotherapy Haematological Tumours Molecular Targets Radiation Therapy Solid Tumours Oncology and Carcinogenesis not elsewhere classified Wnt pathway recurrence multifactor dimensionality reduction SNP interactions colorectal cancer Aaron A. Curtis Yajun Yu Megan Carey Patrick Parfrey Yildiz E. Yilmaz Sevtap Savas DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf |
topic_facet |
Cancer Cancer Cell Biology Cancer Diagnosis Cancer Genetics Cancer Therapy (excl. Chemotherapy and Radiation Therapy) Chemotherapy Haematological Tumours Molecular Targets Radiation Therapy Solid Tumours Oncology and Carcinogenesis not elsewhere classified Wnt pathway recurrence multifactor dimensionality reduction SNP interactions colorectal cancer |
description |
Background Interactions among genetic variants are rarely studied but may explain a part of the variability in patient outcomes. Objectives In this study, we aimed to identify 1 to 3 way interactions among SNPs from five Wnt protein interaction networks that predict the 5-year recurrence risk in a cohort of stage I-III colorectal cancer patients. Methods 423 patients recruited to the Newfoundland Familial Colorectal Cancer Registry were included. Five Wnt family member proteins (Wnt1, Wnt2, Wnt5a, Wnt5b, and Wnt11) were selected. The BioGRID database was used to identify the proteins interacting with each of these proteins. Genotypes of the SNPs located in the interaction network genes were retrieved from a genome-wide SNP genotype data previously obtained in the patient cohort. The GMDR 0.9 program was utilized to examine 1-, 2-, and 3-SNP interactions using a 5-fold cross validation step. Top GMDR 0.9 models were assessed by permutation testing and, if significant, prognostic associations were verified by multivariable logistic regression models. Results GMDR 0.9 has identified novel 1, 2, and 3-way SNP interactions associated with 5-year recurrence risk in colorectal cancer. Nine of these interactions were multi loci interactions (2-way or 3-way). Identified interaction models were able to distinguish patients based on their 5-year recurrence-free status in multivariable regression models. The significance of interactions was the highest in the 3-SNP models. Several of the identified SNPs were eQTLs, indicating potential biological roles of the genes they were associated with in colorectal cancer recurrence. Conclusions We identified novel interacting genetic variants that associate with 5-year recurrence risk in colorectal cancer. A significant portion of the genes identified were previously linked to colorectal cancer pathogenesis or progression. These variants and genes are of interest for future functional and prognostic studies. Our results provide further evidence for the utility of GMDR models in ... |
format |
Dataset |
author |
Aaron A. Curtis Yajun Yu Megan Carey Patrick Parfrey Yildiz E. Yilmaz Sevtap Savas |
author_facet |
Aaron A. Curtis Yajun Yu Megan Carey Patrick Parfrey Yildiz E. Yilmaz Sevtap Savas |
author_sort |
Aaron A. Curtis |
title |
DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf |
title_short |
DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf |
title_full |
DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf |
title_fullStr |
DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf |
title_full_unstemmed |
DataSheet_1_Multifactor dimensionality reduction method identifies novel SNP interactions in the WNT protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf |
title_sort |
datasheet_1_multifactor dimensionality reduction method identifies novel snp interactions in the wnt protein interaction networks that are associated with recurrence risk in colorectal cancer.pdf |
publishDate |
2023 |
url |
https://doi.org/10.3389/fonc.2023.1122229.s001 https://figshare.com/articles/dataset/DataSheet_1_Multifactor_dimensionality_reduction_method_identifies_novel_SNP_interactions_in_the_WNT_protein_interaction_networks_that_are_associated_with_recurrence_risk_in_colorectal_cancer_pdf/22267630 |
genre |
Newfoundland |
genre_facet |
Newfoundland |
op_relation |
doi:10.3389/fonc.2023.1122229.s001 https://figshare.com/articles/dataset/DataSheet_1_Multifactor_dimensionality_reduction_method_identifies_novel_SNP_interactions_in_the_WNT_protein_interaction_networks_that_are_associated_with_recurrence_risk_in_colorectal_cancer_pdf/22267630 |
op_rights |
CC BY 4.0 |
op_doi |
https://doi.org/10.3389/fonc.2023.1122229.s001 |
_version_ |
1766109856793624576 |