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Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk.

Publication ,  Journal Article
Brossard, M; Fang, S; Vaysse, A; Wei, Q; Chen, WV; Mohamdi, H; Maubec, E; Lavielle, N; Galan, P; Lathrop, M; Avril, M-F; Lee, JE; Amos, CI ...
Published in: Int J Cancer
October 15, 2015

Genome-wide association studies (GWASs) have characterized 13 loci associated with melanoma, which only account for a small part of melanoma risk. To identify new genes with too small an effect to be detected individually but which collectively influence melanoma risk and/or show interactive effects, we used a two-step analysis strategy including pathway analysis of genome-wide SNP data, in a first step, and epistasis analysis within significant pathways, in a second step. Pathway analysis, using the gene-set enrichment analysis (GSEA) approach and the gene ontology (GO) database, was applied to the outcomes of MELARISK (3,976 subjects) and MDACC (2,827 subjects) GWASs. Cross-gene SNP-SNP interaction analysis within melanoma-associated GOs was performed using the INTERSNP software. Five GO categories were significantly enriched in genes associated with melanoma (false discovery rate ≤ 5% in both studies): response to light stimulus, regulation of mitotic cell cycle, induction of programmed cell death, cytokine activity and oxidative phosphorylation. Epistasis analysis, within each of the five significant GOs, showed significant evidence for interaction for one SNP pair at TERF1 and AFAP1L2 loci (pmeta-int  = 2.0 × 10(-7) , which met both the pathway and overall multiple-testing corrected thresholds that are equal to 9.8 × 10(-7) and 2.0 × 10(-7) , respectively) and suggestive evidence for another pair involving correlated SNPs at the same loci (pmeta-int  = 3.6 × 10(-6) ). This interaction has important biological relevance given the key role of TERF1 in telomere biology and the reported physical interaction between TERF1 and AFAP1L2 proteins. This finding brings a novel piece of evidence for the emerging role of telomere dysfunction into melanoma development.

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Published In

Int J Cancer

DOI

EISSN

1097-0215

Publication Date

October 15, 2015

Volume

137

Issue

8

Start / End Page

1901 / 1909

Location

United States

Related Subject Headings

  • Telomere-Binding Proteins
  • Skin Neoplasms
  • Signal Transduction
  • Shelterin Complex
  • Polymorphism, Single Nucleotide
  • Oncology & Carcinogenesis
  • Melanoma
  • Humans
  • Genome-Wide Association Study
  • Genetic Predisposition to Disease
 

Citation

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Brossard, M., Fang, S., Vaysse, A., Wei, Q., Chen, W. V., Mohamdi, H., … Demenais, F. (2015). Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk. Int J Cancer, 137(8), 1901–1909. https://doi.org/10.1002/ijc.29570
Brossard, Myriam, Shenying Fang, Amaury Vaysse, Qingyi Wei, Wei V. Chen, Hamida Mohamdi, Eve Maubec, et al. “Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk.Int J Cancer 137, no. 8 (October 15, 2015): 1901–9. https://doi.org/10.1002/ijc.29570.
Brossard M, Fang S, Vaysse A, Wei Q, Chen WV, Mohamdi H, et al. Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk. Int J Cancer. 2015 Oct 15;137(8):1901–9.
Brossard, Myriam, et al. “Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk.Int J Cancer, vol. 137, no. 8, Oct. 2015, pp. 1901–09. Pubmed, doi:10.1002/ijc.29570.
Brossard M, Fang S, Vaysse A, Wei Q, Chen WV, Mohamdi H, Maubec E, Lavielle N, Galan P, Lathrop M, Avril M-F, Lee JE, Amos CI, Demenais F. Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk. Int J Cancer. 2015 Oct 15;137(8):1901–1909.
Journal cover image

Published In

Int J Cancer

DOI

EISSN

1097-0215

Publication Date

October 15, 2015

Volume

137

Issue

8

Start / End Page

1901 / 1909

Location

United States

Related Subject Headings

  • Telomere-Binding Proteins
  • Skin Neoplasms
  • Signal Transduction
  • Shelterin Complex
  • Polymorphism, Single Nucleotide
  • Oncology & Carcinogenesis
  • Melanoma
  • Humans
  • Genome-Wide Association Study
  • Genetic Predisposition to Disease