ArticlePloS one2013
Replication and predictive value of SNPs associated with melanoma and pigmentation traits in a Southern European case-control study.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 3 of them syntheses that pooled it.
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Who cites it
26 citing papers in PubMed, 3 syntheses or guidelines pooled it, 42 citations in OpenAlex.
- Risk Prediction Models for Melanoma: A Systematic Review on the Heterogeneity in Model Development and Validation.International journal of environmental research and public health · 2020Pooled it
- Combining common genetic variants and non-genetic risk factors to predict risk of cutaneous melanoma.Human molecular genetics · 2018Pooled it
- Updated field synopsis and systematic meta-analyses of genetic association studies in cutaneous melanoma: the MelGene database.The Journal of investigative dermatology · 2015Pooled it
- Image feature embedding with a deep learning framework improves genome-wide association studies on dog endophenotypes.Science advances · 2026Article
- Variant ranking pipeline for complex familial disorders.Scientific reports · 2024Article
- Inter-Rater Agreement in Assessing Risk of Bias in Melanoma Prediction Studies Using the Prediction Model Risk of Bias Assessment Tool (PROBAST): Results from a Controlled Experiment on the Effect of Specific Rater Training.Journal of clinical medicine · 2023Article
- Using the Prediction Model Risk of Bias Assessment Tool (PROBAST) to Evaluate Melanoma Prediction Studies.Cancers · 2022Article
- Reporting Quality of Studies Developing and Validating Melanoma Prediction Models: An Assessment Based on the TRIPOD Statement.Healthcare (Basel, Switzerland) · 2022Article
- Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil.BMC cancer · 2020Article
- Assessing the Incremental Contribution of Common Genomic Variants to Melanoma Risk Prediction in Two Population-Based Studies.The Journal of investigative dermatology · 2018Article
- Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study.Human molecular genetics · 2018Article
- Article
- Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.PloS one · 2018Article
- The awakening of the CDK10/Cyclin M protein kinase.Oncotarget · 2017Review
- Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma.The Journal of investigative dermatology · 2016Article
- Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds.Genetics · 2016Article
- Association of common variants inJournal of Cancer · 2016Article
- Indoor tanning and the MC1R genotype: risk prediction for basal cell carcinoma risk in young people.American journal of epidemiology · 2015Article
- Genetic epidemiology of malignant melanoma susceptibility.Melanoma management · 2015Review
- Independent validation of six melanoma risk prediction models.The Journal of investigative dermatology · 2015Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenetic association studies have revealed numerous polymorphisms conferring susceptibility to melanoma. We aimed to replicate previously discovered melanoma-associated single-nucleotide polymorphisms (SNPs) in a Greek case-control population, and examine their predictive value.
methodsBased on a field synopsis of genetic variants of melanoma (MelGene), we genotyped 284 patients and 284 controls at 34 melanoma-associated SNPs of which 19 derived from GWAS. We tested each one of the 33 SNPs passing quality control for association with melanoma both with and without accounting for the presence of well-established phenotypic risk factors. We compared the risk allele frequencies between the Greek population and the HapMap CEU sample. Finally, we evaluated the predictive ability of the replicated SNPs.
resultsRisk allele frequencies were significantly lower compared to the HapMap CEU for eight SNPs (rs16891982--SLC45A2, rs12203592--IRF4, rs258322--CDK10, rs1805007--MC1R, rs1805008--MC1R, rs910873--PIGU, rs17305573--PIGU, and rs1885120--MTAP) and higher for one SNP (rs6001027--PLA2G6) indicating a different profile of genetic susceptibility in the studied population. Previously identified effect estimates modestly correlated with those found in our population (r = 0.72, P<0.0001). The strongest associations were observed for rs401681-T in CLPTM1L (odds ratio [OR] 1.60, 95% CI 1.22-2.10; P = 0.001), rs16891982-C in SCL45A2 (OR 0.51, 95% CI 0.34-0.76; P = 0.001), and rs1805007-T in MC1R (OR 4.38, 95% CI 2.03-9.43; P = 2×10⁻⁵). Nominally statistically significant associations were seen also for another 5 variants (rs258322-T in CDK10, rs1805005-T in MC1R, rs1885120-C in MYH7B, rs2218220-T in MTAP and rs4911442-G in the ASIP region). The addition of all SNPs with nominal significance to a clinical non-genetic model did not substantially improve melanoma risk prediction (AUC for clinical model 83.3% versus 83.9%, p = 0.66).
conclusionOverall, our study has validated genetic variants that are likely to contribute to melanoma susceptibility in the Greek population.
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