scholarly journals Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer

2015 ◽  
Vol 14s2 ◽  
pp. CIN.S17289
Author(s):  
Rajesh Talluri ◽  
Sanjay Shete
Keyword(s):  
Information Theory ◽  
Logistic Regression ◽  
Head And Neck Cancer ◽  
Head And Neck ◽  
Neck Cancer ◽  
Genome Wide Association Study ◽  
Interaction Effects ◽  
Theory Approach ◽  
Nucleotide Polymorphisms ◽  
Regression Approach

Epistasis helps to explain how multiple single-nucleotide polymorphisms (SNPs) interact to cause disease. A variety of tools have been developed to detect epistasis. In this article, we explore the strengths and weaknesses of an information theory approach for detecting epistasis and compare it to the logistic regression approach through simulations. We consider several scenarios to simulate the involvement of SNPs in an epistasis network with respect to linkage disequilibrium patterns among them and the presence or absence of main and interaction effects. We conclude that the information theory approach more efficiently detects interaction effects when main effects are absent, whereas, in general, the logistic regression approach is appropriate in all scenarios but results in higher false positives. We compute epistasis networks for SNPs in the FSD1L gene using a two-phase head and neck cancer genome-wide association study involving 2,185 cases and 4,507 controls to demonstrate the practical application of the methods.

scholarly journals Effects of in IL-1B/IL-1RN variants on the susceptibility to head and neck cancer in a chinese Han population

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanhai Yin ◽  
Fen Li ◽  
Liangqian Tong ◽  
Chunru Chen ◽  
Bo Yuan
Keyword(s):  
Logistic Regression ◽  
Head And Neck Cancer ◽  
Head And Neck ◽  
Genetic Association ◽  
Neck Cancer ◽  
Chinese Han Population ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Han Population ◽  
Logistic Regression Models

Abstract Background The study aimed to evaluate the relationship of IL-1B/IL-1RN polymorphisms to the predisposition of head and neck cancer (HNC) in a Chinese Han population. Methods Nine single-nucleotide polymorphisms (SNPs) in IL-1B/IL-1RN were genotyped based on Agena MassARRAY platform. Logistic regression models were used to analyze the genetic association between these SNPs and HNC risk by calculating odds ratios (ORs) and 95% confidence intervals (CI). Haplotype analysis were performed using Haploview program and logistic regression model. Results The genetic association between rs1143643 in IL-1B and the higher risk of HNC was found (OR = 1.23, 95% CI 1.04–1.46) in the overall. IL-1RN rs17042888 was related to a reduced risk of HNC in the subjects aged > 46 years (OR = 0.70, 95% CI: 0.50–0.98) and in females (OR = 0.71, 95% CI 0.52–0.98), while rs1143643 increased the predisposition of HNC among females (OR = 1.76, 95% CI 1.13–2.74). Furthermore, rs1143643 had an increased susceptibility to thyroid carcinoma (OR = 1.61, 95% CI 1.10–2.34). Moreover, compared with stage I–II, the frequency of IL-1RN rs452204-AG genotype was lower in patients with stage III–IV. Conclusions IL-1B (rs1143643) and IL-1RN (rs17042888 and rs452204) polymorphisms might be related to the individual susceptibility of HNC in the Chinese Han population. These results might help to improve the understanding of IL-1B and IL-1RN genes in the occurrence of HNC.

Relationship of single nucleotide polymorphisms and haplotype interaction of mitochondrial unfolded protein response pathway genes with head and neck cancer

2019 ◽  
Vol 15 (33) ◽  
pp. 3819-3829
Author(s):  
Malik Waqar Ahmed ◽  
Ishrat Mahjabeen ◽  
Shazma Gul ◽  
Anum Khursheed ◽  
Azhar Mehmood ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Head And Neck ◽  
Unfolded Protein Response ◽  
Neck Cancer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Unfolded Protein ◽  
Protein Response ◽  
Mitochondrial Unfolded Protein Response

Aim: In this study, we evaluated the effect of selected polymorphisms of mitochondrial unfolded protein response (UPRmt) pathway in 500 head and neck cancer (HNC) patients and 500 healthy controls from Pakistan. Materials & methods: The experiments were conducted using tetra-ARMS PCR followed by DNA sequencing. Results: Multivariate analysis showed that AA genotype of rs3782116 showed fivefold, GG genotype of rs6598072 approximately twofold and CC genotype of rs4946936 and TT genotype of rs12212067 showed twofold increased risk of HNC. Furthermore, haplotype analysis showed that certain haplotypes of UPRmt pathway single nucleotide polymorphisms have significant association with increased HNC risk. Conclusion: These results show that genetic aberrations in UPRmt pathway genes have association with increased HNC risk and can be an indicator of advance clinical outcome especially invasion and metastasis.

XPC, XPD/ERCC2, UMPS, CYP1b1 and XRCC5, single nucleotide polymorphisms (SNPs) in head and neck cancer

2004 ◽  
Vol 22 (14_suppl) ◽  
pp. 5588-5588
Author(s):  
J. Carles ◽  
M. Monzo ◽  
R. Artells ◽  
M. Amat ◽  
P. Foro ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Head And Neck ◽  
Neck Cancer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Single Nucleotide Polymorphisms of XRCC1 and the Risk of Head and Neck Cancer

2018 ◽  
Author(s):  
VV Narayana Rao ◽  
Sailaja Boddikuri ◽  
Vishnuvardhan Zakkula ◽  
Madan Ranjith Pusapati ◽  
Kereena Chukka
Keyword(s):  
Head And Neck Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Head And Neck ◽  
Neck Cancer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Immunologic determinants of head and neck cancer response to induction chemotherapy.

1989 ◽  
Vol 7 (7) ◽  
pp. 857-864 ◽  
Author(s):  
S P Schantz ◽  
H E Savage ◽  
T Racz ◽  
F J Liu ◽  
B W Brown ◽  
...  
Keyword(s):  
Immune Response ◽  
Logistic Regression ◽  
Regression Analysis ◽  
Head And Neck Cancer ◽  
Head And Neck ◽  
Cancer Patients ◽  
Induction Chemotherapy ◽  
Neck Cancer ◽  
Logistic Regression Analysis ◽  
Total Immunoglobulin

Various measures of immune response were assessed prior to induction chemotherapy (intravenous [IV] cisplatin, fluorouracil [5-FU], and bleomycin) in 43 previously untreated head and neck cancer patients to derive a clinical response prediction model. These were parameters of functional cellular immunity (natural killer [NK] cell activity, lymphocyte blastogenesis response to mitogens), total lymphocyte and lymphocyte subset numbers and percentages, and circulating humoral immunity (total immunoglobulin, immunoglobulin classes, and C1q binding activity [C1q BA]). The C1q BA may reflect levels of circulating immune complexes within peripheral blood. The objective primary tumor response rate was 65% (16 complete responses and 12 partial responses). Univariate logistic regression analysis showed that failure to respond to therapy was significantly related to higher value (vis-à-vis response) of humoral immune parameters total immunoglobulin (Ig), P less than .01; IgG, P less than .01; and C1q BA, P less than .001. No association between cellular immune response measurements and response to chemotherapy was identified. By multivariate logistic regression analysis, only C1q BA levels were predictive of drug therapy responsiveness (P less than .001). Results extend our previous investigations regarding C1q BA measurement in head and neck cancer patients, and show that C1q BA levels add accuracy of prediction of subsequent chemotherapy response to that based solely on standard staging criteria and other parameters of immune status.

XPC, XPD/ERCC2, UMPS, CYP1b1 and XRCC5, single nucleotide polymorphisms (SNPs) in head and neck cancer

2004 ◽  
Vol 22 (14_suppl) ◽  
pp. 5588-5588 ◽  
Author(s):  
J. Carles ◽  
M. Monzo ◽  
R. Artells ◽  
M. Amat ◽  
P. Foro ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Head And Neck ◽  
Neck Cancer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
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