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SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns.
- Source :
-
Bioinformatics (Oxford, England) [Bioinformatics] 2017 Mar 15; Vol. 33 (6), pp. 822-833. - Publication Year :
- 2017
-
Abstract
- Motivation: Testing SNP-SNP interactions is considered as a key for overcoming bottlenecks of genetic association studies. However, related statistical methods for testing SNP-SNP interactions are underdeveloped.<br />Results: We propose the SNP Interaction Pattern Identifier (SIPI), which tests 45 biologically meaningful interaction patterns for a binary outcome. SIPI takes non-hierarchical models, inheritance modes and mode coding direction into consideration. The simulation results show that SIPI has higher power than MDR (Multifactor Dimensionality Reduction), AA&#95;Full, Geno&#95;Full (full interaction model with additive or genotypic mode) and SNPassoc in detecting interactions. Applying SIPI to the prostate cancer PRACTICAL consortium data with approximately 21 000 patients, the four SNP pairs in EGFR-EGFR , EGFR-MMP16 and EGFR-CSF1 were found to be associated with prostate cancer aggressiveness with the exact or similar pattern in the discovery and validation sets. A similar match for external validation of SNP-SNP interaction studies is suggested. We demonstrated that SIPI not only searches for more meaningful interaction patterns but can also overcome the unstable nature of interaction patterns.<br />Availability and Implementation: The SIPI software is freely available at http://publichealth.lsuhsc.edu/LinSoftware/ .<br />Contact: hlin1@lsuhsc.edu.<br />Supplementary Information: Supplementary data are available at Bioinformatics online.<br /> (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com)
- Subjects :
- ErbB Receptors genetics
Genetic Predisposition to Disease
Humans
Male
Matrix Metalloproteinase 16 genetics
Models, Genetic
Prostatic Neoplasms metabolism
Epistasis, Genetic
Genetic Association Studies methods
Polymorphism, Single Nucleotide
Prostatic Neoplasms genetics
Software
Statistics as Topic
Subjects
Details
- Language :
- English
- ISSN :
- 1367-4811
- Volume :
- 33
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- Bioinformatics (Oxford, England)
- Publication Type :
- Academic Journal
- Accession number :
- 28039167
- Full Text :
- https://doi.org/10.1093/bioinformatics/btw762