Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method
Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene...
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BioMed Central
2016-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-14-166.pdf |
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| author | Seungyeoun Lee Donghee Son Wenbao Yu Taesung Park |
| author_facet | Seungyeoun Lee Donghee Son Wenbao Yu Taesung Park |
| author_sort | Seungyeoun Lee |
| collection | DOAJ |
| description | Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene interactions, rather than a single-locus approach. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely applied, since the constructive induction algorithm of MDR efficiently reduces high-order dimensions into one dimension by classifying multi-level genotypes into high- and low-risk groups. The MDR method has been extended to various phenotypes and has been improved to provide a significance test for gene-gene interactions. In this paper, we propose a simple method, called accelerated failure time (AFT) UM-MDR, in which the idea of a unified model-based MDR is extended to the survival phenotype by incorporating AFT-MDR into the classification step. The proposed AFT UM-MDR method is compared with AFT-MDR through simulation studies, and a short discussion is given. |
| format | Article |
| id | doaj-art-7d80997722054a308ca5ebf2f964778d |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2016-12-01 |
| publisher | BioMed Central |
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| series | Genomics & Informatics |
| spelling | doaj-art-7d80997722054a308ca5ebf2f964778d2025-02-02T17:25:34ZengBioMed CentralGenomics & Informatics1598-866X2234-07422016-12-0114416617210.5808/GI.2016.14.4.166171Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction MethodSeungyeoun Lee0Donghee Son1Wenbao Yu2Taesung Park3Department of Mathematics and Statistics, Sejong University, Seoul 05006, Korea.Department of Mathematics and Statistics, Sejong University, Seoul 05006, Korea.Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.Department of Statistics, Seoul National University, Seoul 08826, Korea.Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene interactions, rather than a single-locus approach. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely applied, since the constructive induction algorithm of MDR efficiently reduces high-order dimensions into one dimension by classifying multi-level genotypes into high- and low-risk groups. The MDR method has been extended to various phenotypes and has been improved to provide a significance test for gene-gene interactions. In this paper, we propose a simple method, called accelerated failure time (AFT) UM-MDR, in which the idea of a unified model-based MDR is extended to the survival phenotype by incorporating AFT-MDR into the classification step. The proposed AFT UM-MDR method is compared with AFT-MDR through simulation studies, and a short discussion is given.http://genominfo.org/upload/pdf/gni-14-166.pdfaccelerated failure time modelgene-gene interactionmultifactor dimensionality reduction methodsurvival phenotype |
| spellingShingle | Seungyeoun Lee Donghee Son Wenbao Yu Taesung Park Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method Genomics & Informatics accelerated failure time model gene-gene interaction multifactor dimensionality reduction method survival phenotype |
| title | Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method |
| title_full | Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method |
| title_fullStr | Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method |
| title_full_unstemmed | Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method |
| title_short | Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method |
| title_sort | gene gene interaction analysis for the accelerated failure time model using a unified model based multifactor dimensionality reduction method |
| topic | accelerated failure time model gene-gene interaction multifactor dimensionality reduction method survival phenotype |
| url | http://genominfo.org/upload/pdf/gni-14-166.pdf |
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