The interaction of four genes in the inflammation pathway significantly predicts prostate cancer risk.
It is widely hypothesized that the interactions of multiple genes influence individual risk to prostate cancer. However, current efforts at identifying prostate cancer risk genes primarily rely on single-gene approaches. In an attempt to fill this gap, we carried out a study to explore the joint effect of multiple genes in the inflammation pathway on prostate cancer risk. We studied 20 genes in the Toll-like receptor signaling pathway as well as several cytokines. For each of these genes, we selected and genotyped haplotype-tagging single nucleotide polymorphisms (SNP) among 1,383 cases and 780 controls from the CAPS (CAncer Prostate in Sweden) study population. A total of 57 SNPs were included in the final analysis. A data mining method, multifactor dimensionality reduction, was used to explore the interaction effects of SNPs on prostate cancer risk. Interaction effects were assessed for all possible n SNP combinations, where n = 2, 3, or 4. For each n SNP combination, the model providing lowest prediction error among 100 cross-validations was chosen. The statistical significance levels of the best models in each n SNP combination were determined using permutation tests. A four-SNP interaction (one SNP each from IL-10, IL-1RN, TIRAP, and TLR5) had the lowest prediction error (43.28%, P = 0.019). Our ability to analyze a large number of SNPs in a large sample size is one of the first efforts in exploring the effect of high-order gene-gene interactions on prostate cancer risk, and this is an important contribution to this new and quickly evolving field.
Xu
Jianfeng
J
Center for Human Genomics, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA. jxu@wfubmc.edu
Lowey
James
J
Wiklund
Fredrik
F
Sun
Jielin
J
Lindmark
Fredrik
F
Hsu
Fang-Chi
FC
Dimitrov
Latchezar
L
Chang
Baoli
B
Turner
Aubrey R
AR
Liu
Wennan
W
Adami
Hans-Olov
HO
Suh
Edward
E
Moore
Jason H
JH
Zheng
S Lilly
SL
Isaacs
William B
WB
Trent
Jeffrey M
JM
Grönberg
Henrik
H
D016022:Case-Control Studies; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007249:Inflammation; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011379:Prognosis; D011471:Prostatic Neoplasms / Q000209:etiology / Q000235:genetics* / Q000276:immunology*; D012042:Registries / Q000706:statistics & numerical data; D012307:Risk Factors; D015398:Signal Transduction; D051193:Toll-Like Receptors / Q000235:genetics*
D051193:Toll-Like Receptors