dc.contributor.author | Lin, H-Y | |
dc.contributor.author | Chen, D-T | |
dc.contributor.author | Huang, P-Y | |
dc.contributor.author | Liu, Y-H | |
dc.contributor.author | Ochoa, A | |
dc.contributor.author | Zabaleta, J | |
dc.contributor.author | Mercante, DE | |
dc.contributor.author | Fang, Z | |
dc.contributor.author | Sellers, TA | |
dc.contributor.author | Pow-Sang, JM | |
dc.contributor.author | Cheng, C-H | |
dc.contributor.author | Eeles, R | |
dc.contributor.author | Easton, D | |
dc.contributor.author | Kote-Jarai, Z | |
dc.contributor.author | Amin Al Olama, A | |
dc.contributor.author | Benlloch, S | |
dc.contributor.author | Muir, K | |
dc.contributor.author | Giles, GG | |
dc.contributor.author | Wiklund, F | |
dc.contributor.author | Gronberg, H | |
dc.contributor.author | Haiman, CA | |
dc.contributor.author | Schleutker, J | |
dc.contributor.author | Nordestgaard, BG | |
dc.contributor.author | Travis, RC | |
dc.contributor.author | Hamdy, F | |
dc.contributor.author | Pashayan, N | |
dc.contributor.author | Khaw, K-T | |
dc.contributor.author | Stanford, JL | |
dc.contributor.author | Blot, WJ | |
dc.contributor.author | Thibodeau, SN | |
dc.contributor.author | Maier, C | |
dc.contributor.author | Kibel, AS | |
dc.contributor.author | Cybulski, C | |
dc.contributor.author | Cannon-Albright, L | |
dc.contributor.author | Brenner, H | |
dc.contributor.author | Kaneva, R | |
dc.contributor.author | Batra, J | |
dc.contributor.author | Teixeira, MR | |
dc.contributor.author | Pandha, H | |
dc.contributor.author | Lu, Y-J | |
dc.contributor.author | PRACTICAL Consortium, | |
dc.contributor.author | Park, JY | |
dc.date.accessioned | 2018-03-01T09:43:27Z | |
dc.date.issued | 2017-03-15 | |
dc.identifier.citation | Bioinformatics (Oxford, England), 2017, 33 (6), pp. 822 - 833 | |
dc.identifier.issn | 1367-4803 | |
dc.identifier.uri | https://repository.icr.ac.uk/handle/internal/1462 | |
dc.identifier.eissn | 1367-4811 | |
dc.identifier.doi | 10.1093/bioinformatics/btw762 | |
dc.description.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. 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_Full, Geno_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. AVAILABILITY AND IMPLEMENTATION: The SIPI software is freely available at http://publichealth.lsuhsc.edu/LinSoftware/ . CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. | |
dc.format | Print | |
dc.format.extent | 822 - 833 | |
dc.language | eng | |
dc.language.iso | eng | |
dc.publisher | OXFORD UNIV PRESS | |
dc.rights.uri | https://www.rioxx.net/licenses/all-rights-reserved | |
dc.subject | PRACTICAL Consortium | |
dc.subject | Humans | |
dc.subject | Prostatic Neoplasms | |
dc.subject | Genetic Predisposition to Disease | |
dc.subject | Epistasis, Genetic | |
dc.subject | Polymorphism, Single Nucleotide | |
dc.subject | Models, Genetic | |
dc.subject | Software | |
dc.subject | Male | |
dc.subject | Matrix Metalloproteinase 16 | |
dc.subject | Statistics as Topic | |
dc.subject | Genetic Association Studies | |
dc.subject | ErbB Receptors | |
dc.title | SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns. | |
dc.type | Journal Article | |
dcterms.dateAccepted | 2016-11-28 | |
rioxxterms.versionofrecord | 10.1093/bioinformatics/btw762 | |
rioxxterms.licenseref.uri | https://www.rioxx.net/licenses/all-rights-reserved | |
rioxxterms.licenseref.startdate | 2017-03 | |
rioxxterms.type | Journal Article/Review | |
dc.relation.isPartOf | Bioinformatics (Oxford, England) | |
pubs.issue | 6 | |
pubs.notes | Not known | |
pubs.organisational-group | /ICR | |
pubs.organisational-group | /ICR/Primary Group | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Genetics and Epidemiology | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Genetics and Epidemiology/Oncogenetics | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Radiotherapy and Imaging | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Radiotherapy and Imaging/Oncogenetics | |
pubs.organisational-group | /ICR | |
pubs.organisational-group | /ICR/Primary Group | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Genetics and Epidemiology | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Genetics and Epidemiology/Oncogenetics | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Radiotherapy and Imaging | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Radiotherapy and Imaging/Oncogenetics | |
pubs.publication-status | Published | |
pubs.volume | 33 | |
pubs.embargo.terms | Not known | |
icr.researchteam | Oncogenetics | |
dc.contributor.icrauthor | Eeles, Rosalind | |
dc.contributor.icrauthor | Kote-Jarai, Zsofia | |