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. 2020 Nov 9;20(1):1069.
doi: 10.1186/s12885-020-07485-x.

Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil

Larissa B Reis  1   2 , Renato M Bakos  2   3 , Fernanda S L Vianna  1   4 , Gabriel S Macedo  1 , Vanessa C Jacovas  4 , André M Ribeiro-Dos-Santos  5 , Sidney Santos  5 , Lúcio Bakos  3 , Patricia Ashton-Prolla  6   7   8
Affiliations

Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil

Larissa B Reis et al. BMC Cancer. .

Abstract

Background: Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited.

Methods: In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis.

Results: Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10- 3), with a redundant effect.

Conclusions: These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.

Keywords: Melanoma; Pigmentation; SNPs.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Multifactor dimensionality reduction (MDR) interaction models. Interaction circle graph comprised of nodes with pairwise connections. Values in nodes represent information gain (IG) of individual genes. While values between nodes are the IG of each pairwise combination. The type of interaction is showed by color of the line. The blue line represents negative entropy. Redundancy or linkage disequilibrium
Fig. 2
Fig. 2
The SNPs interaction to risk with melanoma development. A high-frequency genotype combination is displayed in Dark Square. while low-frequency combinations are in lightly shaded. For each cell. The left bar indicates the absolute number of cases and the right bar the absolute number of controls. a The effect of HERC2 rs1129038AA genotype. b The combination effect of SLC24A5 rs1426654AA and SLC45A2 rs16891982GG genotypes. c The combination effect of SLC24A5 rs1426654AA. SLC45A2 rs16891982GG. and HERC2 rs1129038AA genotypes
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