An empirical fuzzy multifactor dimensionality reduction method for detecting gene-gene interactions

Leem, Sangseob; Park, Taesung

doi:10.1186/s12864-017-3496-x

Cited by 31 publications

(27 citation statements)

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“…Lazzerini et al 17 reported that IL-1β-induced IL-6 production from human cultured osteoblasts might provide a rationale for the possible employment of rosuvastatin in the treatment of osteoporosis. In addition, Lee et al 18 showed that osteoclastogenesis by IL-1β and/or endoplasmic reticulum stress was mainly associated with up-regulation of eIF2α, GRP78, PERK and IRE1, suggesting that it might be a new therapeutic target for osteoporosis. There is increasing evidence that IL-1β might play an important role in the pathogenesis of osteoporosis.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of genetic variants in IL‐1B and its interaction with the predisposition of osteoporosis in the northwestern Chinese Han population

Sun

et al. 2020

The Journal of Gene Medicine

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Background: Interleukin (IL)-1β stimulates the proliferation and differentiation of osteoclast precursors into mature osteoclasts. IL-1B polymorphisms may influence the gene and protein expression of IL-1β. The present study aimed to investigate the association of IL-1B variants (rs2853550, rs1143643, rs3136558, rs1143630, rs1143627, rs16944 and rs1143623) and their interaction with osteoporosis risk among the northwestern Chinese Han population. Methods: AN Agena MassARRAY system (Agena, San Diego, CA, USA) was employed for genotyping in 594 osteoporosis patients and 599 healthy controls. The possible association between IL-1B polymorphisms and risks of osteoporosis development was identified with odds ratios (OR) and 95% confidence intervals (CI) using logistic regression models. Haplotype analysis and multifactor dimension reduction analysis were used to explore the potential association between combined single nucleotide polymorphisms (SNPs) and osteoporosis risk. Results: The AA genotype of rs2853550 was a protective factor for osteoporosis occurrence (OR = 0.11, p = 0.038), whereas rs16944 (OR = 1.19, p = 0.037) and rs1143623 (OR = 1.21, p = 0.025) conferred an increased risk of osteoporosis. Moreover, rs1143627, rs16944 and rs1143623 were associated with an elevated susceptibility to osteoporosis, especially in females and individuals aged > 60 years or with a body mass index > 24 kg/m 2. Haplotype G rs1143630 A rs1143627 G rs16944 was a risk factor of osteoporosis occurrence (OR = 1.20, p = 0.032). The best model of SNP-SNP analysis was a four-locus combination of rs1143643, rs3136558, rs1143630 and rs1143623 (testing accuracy = 0.5623). Conclusions: IL-1B polymorphisms and haplotype G rs1143630 A rs1143627 G rs16944 might contribute to susceptibility to osteoporosis. The SNP-SNP interaction of polymorphisms in IL-1B revealed the accumulated effect on osteoporosis risk.

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Section: Introductionmentioning

confidence: 99%

Evaluation of genetic variants in IL‐1B and its interaction with the predisposition of osteoporosis in the northwestern Chinese Han population

Sun

et al. 2020

The Journal of Gene Medicine

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“…2) was performed to analyze the interactions between SNP and SNP in the CHD risk (22). The difference in clinical characteristics among different genotypes was analyzed using the one-way analysis and ANOVA test.…”

Section: Discussionmentioning

confidence: 99%

Contribution of IL9, IL2RA and IL2RB genetic polymorphisms in coronary heart disease in Chinese Han population

Chen

Wang

Zhang

et al. 2019

Preprint

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Background: Coronary heart disease (CHD) is one of the leading causes of disability and death worldwide. In the pathogenesis of CHD, inflammatory cytokines take an essential part. This study was designed to detect the potential association between IL-9, IL-2RA and IL-2RB variants and CHD in Chinese Han population. Methods: This case-control study conducted 499 CHD patients and 496 healthy controls. Seven selected SNPs were genotyped to investigate the possible association between the polymorphisms and the CHD risk. The interaction of SNP-SNP in the CHD risk was analyzed by Multifactor dimensionality reduction (MDR). Results: We observed an association between IL-9 rs55692658 (OR = 1.72, p = 0.003) and the increased CHD risk. The stratification analysis by age indicated that no matter participants who were older or younger than 61 years, IL-9 rs55692658 and IL-2RB rs1573673 contributed to the CHD susceptibility significantly (p < 0.05, respectively). IL-9 rs55692658 showed an increasing-risk effect (OR = 2.32, p = 0.003), while IL-2RA rs12722498 was correlated with the decreased susceptibility of CHD (OR = 0.54, p = 0.033) in female. Furthermore, IL-2RA rs12569923 was related to the diabetes risk in the CHD patients (OR = 1.50, p = 0.028). MDR analysis revealed a positive interaction between the SNPs. Conclusion: The present study firstly demonstrated that IL-9 rs55692658，IL-2RA rs12569923, rs12722498 and IL-2RB rs3218264 polymorphisms might be related to CHD. The results required further validation by larger studies.

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“…The association was also evaluated in subgroup analyses strati ed by demographic and clinic variables. Multifactor dimensionality reduction (MDR) (version 3.0.2) was performed to evaluate the SNP-SNP interactions in the risk of cervical cancer (14). A two-tailed p-value < 0.05 was considered to be statistically signi cant for all the analyses.…”

Section: Study Participantsmentioning

confidence: 99%

Genetic Polymorphisms of PGF and TNFAIP2 Genes Related to Cervical Cancer Risk Among Uygur Females from China

Ainiwaer

Maisaidi

Liu

et al. 2020

Preprint

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Abstract Background: PGF and TNFAIP2 are important angiogenic factors, which were abnormal expression in cervical cancer (CC). However, no report was investigating the associations between the polymorphisms in the PGF and TNFAIP2 genes and CC risk. Methods: We conducted a case-control study of 342 CC patients and 498 cancer-free controls in Chinese Uygur female population. Three selected SNPs (PGF rs8019391, PGF rs2268615, and TNFAIP2 rs710100) were genotyped to investigate the possible association of the polymorphisms in PGF and TNFAIP2 with the risk of CC. The analysis adjusted by age was used to assess associations of these SNPs with CC risk. Results: PGF rs2268615 (OR = 1.39, 95% CI = 1.04-1.86, p = 0.024) and TNFAIP2 rs710100 (OR = 1.44, 95% CI =1.07-1.95, p = 0.018) polymorphisms were significantly associated with the increased risk of CC. Moreover, PGF rs8019391 T allele was highly represented in patients with III–IV tumor stage (OR = 2.17, p = 4.58´10-4). MDR analysis revealed a positive interaction between the SNPs. Conclusion: Our data suggested that PGF rs2268615, and TNFAIP2 rs710100 polymorphisms may be risk factors for susceptibility to CC, which contributed to the increased risk of CC, and this finding requires further validation by larger studies.Trail registration: Not applicable.

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An empirical fuzzy multifactor dimensionality reduction method for detecting gene-gene interactions

Cited by 31 publications

References 50 publications

Evaluation of genetic variants in IL‐1B and its interaction with the predisposition of osteoporosis in the northwestern Chinese Han population

Evaluation of genetic variants in IL‐1B and its interaction with the predisposition of osteoporosis in the northwestern Chinese Han population

Contribution of IL9, IL2RA and IL2RB genetic polymorphisms in coronary heart disease in Chinese Han population

Genetic Polymorphisms of PGF and TNFAIP2 Genes Related to Cervical Cancer Risk Among Uygur Females from China

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