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 eff...

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Veröffentlicht in:Cancer epidemiology, biomarkers & prevention biomarkers & prevention, 2005-11, Vol.14 (11), p.2563-2568
Hauptverfasser: JIANFENG XU, LOWEY, James, ADAMI, Hans-Olov, SUH, Edward, MOORE, Jason H, ZHENG, S. Lilly, ISAACS, William B, TRENT, Jeffrey M, GRÖNBERG, Henrik, WIKLUND, Fredrik, JIELIN SUN, LINDMARK, Fredrik, HSU, Fang-Chi, DIMITROV, Latchezar, BAOLI CHANG, TURNER, Aubrey R, WENNAN LIU
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container_end_page 2568
container_issue 11
container_start_page 2563
container_title Cancer epidemiology, biomarkers & prevention
container_volume 14
creator JIANFENG XU
LOWEY, James
ADAMI, Hans-Olov
SUH, Edward
MOORE, Jason H
ZHENG, S. Lilly
ISAACS, William B
TRENT, Jeffrey M
GRÖNBERG, Henrik
WIKLUND, Fredrik
JIELIN SUN
LINDMARK, Fredrik
HSU, Fang-Chi
DIMITROV, Latchezar
BAOLI CHANG
TURNER, Aubrey R
WENNAN LIU
description 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 ( CA ncer P rostate in S weden) 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.
doi_str_mv 10.1158/1055-9965.EPI-05-0356
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Lilly ; ISAACS, William B ; TRENT, Jeffrey M ; GRÖNBERG, Henrik ; WIKLUND, Fredrik ; JIELIN SUN ; LINDMARK, Fredrik ; HSU, Fang-Chi ; DIMITROV, Latchezar ; BAOLI CHANG ; TURNER, Aubrey R ; WENNAN LIU</creator><creatorcontrib>JIANFENG XU ; LOWEY, James ; ADAMI, Hans-Olov ; SUH, Edward ; MOORE, Jason H ; ZHENG, S. Lilly ; ISAACS, William B ; TRENT, Jeffrey M ; GRÖNBERG, Henrik ; WIKLUND, Fredrik ; JIELIN SUN ; LINDMARK, Fredrik ; HSU, Fang-Chi ; DIMITROV, Latchezar ; BAOLI CHANG ; TURNER, Aubrey R ; WENNAN LIU</creatorcontrib><description>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 ( CA ncer P rostate in S weden) 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). 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Lilly</creatorcontrib><creatorcontrib>ISAACS, William B</creatorcontrib><creatorcontrib>TRENT, Jeffrey M</creatorcontrib><creatorcontrib>GRÖNBERG, Henrik</creatorcontrib><creatorcontrib>WIKLUND, Fredrik</creatorcontrib><creatorcontrib>JIELIN SUN</creatorcontrib><creatorcontrib>LINDMARK, Fredrik</creatorcontrib><creatorcontrib>HSU, Fang-Chi</creatorcontrib><creatorcontrib>DIMITROV, Latchezar</creatorcontrib><creatorcontrib>BAOLI CHANG</creatorcontrib><creatorcontrib>TURNER, Aubrey R</creatorcontrib><creatorcontrib>WENNAN LIU</creatorcontrib><title>The Interaction of Four Genes in the Inflammation Pathway Significantly Predicts Prostate Cancer Risk</title><title>Cancer epidemiology, biomarkers &amp; prevention</title><addtitle>Cancer Epidemiol Biomarkers Prev</addtitle><description>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 ( CA ncer P rostate in S weden) 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.</description><subject>association</subject><subject>Biological and medical sciences</subject><subject>Case-Control Studies</subject><subject>data mining</subject><subject>Genetic Predisposition to Disease</subject><subject>Genotype</subject><subject>Haplotypes</subject><subject>Humans</subject><subject>Inflammation</subject><subject>Male</subject><subject>MDR</subject><subject>Medical sciences</subject><subject>Medicin och hälsovetenskap</subject><subject>Nephrology. Urinary tract diseases</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Prognosis</subject><subject>prostate cancer</subject><subject>Prostatic Neoplasms - etiology</subject><subject>Prostatic Neoplasms - genetics</subject><subject>Prostatic Neoplasms - immunology</subject><subject>Registries - statistics &amp; numerical data</subject><subject>Risk Factors</subject><subject>Signal Transduction</subject><subject>SNPs</subject><subject>Toll-Like Receptors - genetics</subject><subject>Tumors</subject><subject>Tumors of the urinary system</subject><subject>Urinary tract. 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Lilly</au><au>ISAACS, William B</au><au>TRENT, Jeffrey M</au><au>GRÖNBERG, Henrik</au><au>WIKLUND, Fredrik</au><au>JIELIN SUN</au><au>LINDMARK, Fredrik</au><au>HSU, Fang-Chi</au><au>DIMITROV, Latchezar</au><au>BAOLI CHANG</au><au>TURNER, Aubrey R</au><au>WENNAN LIU</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Interaction of Four Genes in the Inflammation Pathway Significantly Predicts Prostate Cancer Risk</atitle><jtitle>Cancer epidemiology, biomarkers &amp; prevention</jtitle><addtitle>Cancer Epidemiol Biomarkers Prev</addtitle><date>2005-11-01</date><risdate>2005</risdate><volume>14</volume><issue>11</issue><spage>2563</spage><epage>2568</epage><pages>2563-2568</pages><issn>1055-9965</issn><eissn>1538-7755</eissn><abstract>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 ( CA ncer P rostate in S weden) 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. 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source MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; American Association for Cancer Research
subjects association
Biological and medical sciences
Case-Control Studies
data mining
Genetic Predisposition to Disease
Genotype
Haplotypes
Humans
Inflammation
Male
MDR
Medical sciences
Medicin och hälsovetenskap
Nephrology. Urinary tract diseases
Polymorphism, Single Nucleotide
Prognosis
prostate cancer
Prostatic Neoplasms - etiology
Prostatic Neoplasms - genetics
Prostatic Neoplasms - immunology
Registries - statistics & numerical data
Risk Factors
Signal Transduction
SNPs
Toll-Like Receptors - genetics
Tumors
Tumors of the urinary system
Urinary tract. Prostate gland
title The Interaction of Four Genes in the Inflammation Pathway Significantly Predicts Prostate Cancer Risk
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