SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns.

Paper Info

Title
SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns.

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.

Year	DOI	Venue
2017	10.1093/bioinformatics/btw762	BIOINFORMATICS
Field	DocType	Volume
World Wide Web,Identifier,Multifactor dimensionality reduction,Computer science,Computational biology,Bioinformatics,SNP	Journal	33
Issue	ISSN	Citations
6	1367-4803	2
PageRank	References	Authors
0.44	3	42

Authors (42 rows)

Cited by (2 rows)

References (3 rows)

Name	Order	Citations	PageRank
Hui-Yi Lin	1	4	1.92
Dung-Tsa Chen	2	20	4.26
Po-Yu Huang	3	4	3.51
Yung-Hsin Liu	4	2	0.44
Augusto Ochoa	5	2	0.44
Jovanny Zabaleta	6	2	0.44
Donald Mercante	7	5	1.08
Zhide Fang	8	30	4.28
Thomas A. Sellers	9	2	1.12
Julio M. Pow-Sang	10	2	0.78
Chia-Ho Cheng	11	2	0.44
rosalind a eeles	12	4	1.58
Douglas F. Easton	13	15	2.94
Zsofia Kote-Jarai	14	2	0.44
Ali Amin Al Olama	15	2	0.78
Sara Benlloch	16	2	0.44
Kenneth Muir	17	2	1.12
Graham G. Giles	18	2	0.78
Fredrik Wiklund	19	3	1.15
Henrik Gronberg	20	3	1.49
Christopher A Haiman	21	18	3.89
Johanna Schleutker	22	2	0.78
Børge G. Nordestgaard	23	2	0.44
Ruth C. Travis	24	2	0.78
Freddie C. Hamdy	25	3	1.26
Nora Pashayan	26	2	0.78
Kay-Tee Khaw	27	2	0.78
Janet L. Stanford	28	2	0.44
William J. Blot	29	2	0.44
Stephen N. Thibodeau	30	2	0.78
Christiane Maier	31	2	0.78
Adam S. Kibel	32	2	0.78
Cezary Cybulski	33	2	0.44
Lisa A. Cannon-Albright	34	2	0.44
H Brenner	35	4	1.92
Radka Kaneva	36	2	0.44
Jyotsna Batra	37	6	1.48
Manuel R. Teixeira	38	2	1.46
Hardev Pandha	39	2	0.78
Yongjie Lu	40	2	0.78
The PRACTICAL Consortium	41	2	0.44
Jong Y. Park	42	2	0.44