Identification of a melanoma susceptibility locus and somatic mutation in TET2.

Although genetic studies have reported a number of loci associated with melanoma risk, the complex genetic architecture of the disease is not yet fully understood. We sought to identify common genetic variants associated with melanoma risk in a genome-wide association study (GWAS) of 2298 cases and 6654 controls. Thirteen of 15 known loci were replicated with nominal significance. A total of 69 single-nucleotide polymorphisms (SNPs) were selected for in silico replication in two independent melanoma GWAS datasets (a total of 5149 cases and 12 795 controls). Seven novel loci were nominally significantly associated with melanoma risk. These seven SNPs were further genotyped in 234 melanoma cases and 238 controls. The SNP rs4698934 was nominally significantly associated with melanoma risk. The combined odds ratio per T allele = 1.18; 95% confidence interval (1.10-1.25); combined P = 7.70 × 10(-) (7). This SNP is located in the intron of the TET2 gene on chromosome 4q24. In addition, a novel somatic mutation of TET2 was identified by next-generation sequencing in 1 of 22 sporadic melanoma cases. TET2 encodes a member of TET family enzymes that oxidizes 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). It is a putative epigenetic biomarker of melanoma as we previously reported, with observation of reduced TET2 transcriptional expression. This study is the first to implicate TET2 genetic variation and mutation in melanoma.

A mutation hotspot at the p14ARF splice site.

Germline mutations of CDKN2A that affect the p16INK4a transcript have been identified in numerous melanoma pedigrees worldwide. In the UK, over 50% of pedigrees with three or more cases of melanoma have been found to carry mutations of CDKN2A. Mutations that affect p14ARF exon 1beta exclusively are very rare. This has led to the suggestion that it is p16INK4a and not p14ARF that plays the critical role in melanoma predisposition. We report the identification of a cluster of five different germline mutations at the p14ARF exon 1beta splice donor site in melanoma pedigrees. All the five splice site variants showed evidence of being causal mutations. Three of the variants were demonstrated to result in aberrant splicing of the p14ARF mRNA, confirming their role in melanoma predisposition. No other point mutations were identified in the coding region of p14ARF. The p14ARF transcript of CDKN2A is clearly important in disease predisposition in a subset of melanoma pedigrees. Curiously, the only mutations so far reported to affect p14ARF exon 1beta exclusively have been knockout mutations. Further investigation into the spectrum of mutations observed in this gene may help clarify the exact role of p14ARF in melanoma predisposition.

The effect of sun exposure in determining nevus density in UK adolescent twins.

We report a study of 221 teenage twin pairs to examine the genetic and environmental determinants of nevi representing the most potent phenotypic risk factor for melanoma. Our published heritability analysis estimated that nevi are mainly genetically determined. In this paper we examine the role of sun exposure. We report a correlation between nevus density and sun exposure, particularly that acquired in hotter countries than in the UK (mean nevus density 41 per m2 in those in the highest quartile of exposure vs 24 per m2 in those with no exposure, p<0.0001). We were not able to demonstrate a protective effect for either sun protection cream or shirt wearing. By including phenotypic variables and reported sun exposure into the heritability analysis, we conclude that 66% of the total variance of nevus count is attributable to genetic effects: 7% associated to eye color, 6% to hair color, and 1% to reported skin type, which leaves 52% as to yet unidentified genetic factors. Of the 25% of variation attributable to environmental influences, one-third is estimated to be because of sun exposure on hot holidays.

Malignant melanoma in pregnancy.

This article provides a concise overview of issues relating to melanoma and pregnancy, including pregnancy-associated risk and prognosis, and briefly summarizes results from relevant reports that have been published in recent years. The bulk of evidence amassed over the past half century suggests that pregnancy does not significantly affect the risk of developing malignant melanoma. Further, pregnancy does not seem adversely to influence overall survival from the disease. Most studies found no difference in overall survival between pregnant and nonpregnant women with melanoma. Recent reports from large-scale, population-based studies support these conclusions.

Excision margins in the treatment of primary cutaneous melanoma: a systematic review of randomized controlled trials comparing narrow vs wide excision.

BACKGROUND: The optimal excision margin for primary cutaneous melanoma remains controversial, although several clinical studies have suggested that wide local excision is unnecessary. HYPOTHESIS: Wide excision margins do not improve survival in patients with melanoma. OBJECTIVES: To describe the published evidence and determine the effectiveness of wide surgical margins compared with narrow surgical margins. DESIGN: Systematic review of randomized controlled trials that compared narrow margins with wide excision margins for cutaneous melanoma. SETTING: Randomized controlled trials available by March 2001. SUBJECTS: The included trials comprised 2406 participants. INTERVENTION: Surgical excision of melanoma using narrow excision margins compared with excision using wide excision margins. MAIN OUTCOME MEASURE: Effect of width of excision margin on melanoma recurrences, disease-free survival, and overall survival. RESULTS: We identified and analyzed 4 randomized controlled trials. All 4 trials failed to demonstrate statistically significant differences in overall survival and disease-free survival when comparing wide vs narrow excision. Peto pooled odds ratio for overall survival was 0.79 (95% confidence interval, 0.61-1.04) and for disease-free survival was 0.89 (95% confidence interval, 0.69-1.13), indicating a statistically nonsignificant improvement with wide excision. CONCLUSIONS: Not one of the included studies showed any statistically significant difference between the 2 groups treated with narrow or wide excision margins with regard to recurrences and survival. However, current evidence is not sufficient to address the optimal surgical margins for all melanomas, and further research is required.

Association between putative functional variants in the PSMB9 gene and risk of melanoma--re-analysis of published melanoma genome-wide association studies.

To mine possibly hidden causal single-nucleotide polymorphisms (SNPs) of melanoma, we investigated the association of SNPs in 76 M/G1 transition genes with melanoma risk using our published genome-wide association study (GWAS) data set with 1804 melanoma cases and 1026 cancer-free controls. We found multiple SNPs with P < 0.01 and performed validation studies for 18 putative functional SNPs in PSMB9 in two other GWAS data sets. Two SNPs (rs1351383 and rs2127675) were associated with melanoma risk in the GenoMEL data set (P = 0.013 and 0.004, respectively), but failed in validation using the Australian data set. Genotype-phenotype analysis revealed these two SNPs were significantly correlated with mRNA expression level of PSMB9. Further experiments revealed that SNP rs2071480, which is in high LD with rs1351383 and rs2127675, may have a weak effect on the promoter activity of PSMB9. Taken together, our data suggested that functional variants in PSMB9 may contribute to melanoma susceptibility.

Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi.

A high melanocytic nevi count is the strongest known risk factor for cutaneous melanoma. We conducted a genome-wide association study for nevus count using 297,108 SNPs in 1,524 twins, with validation in an independent cohort of 4,107 individuals. We identified strongly associated variants in MTAP, a gene adjacent to the familial melanoma susceptibility locus CDKN2A on 9p21 (rs4636294, combined P = 3.4 x 10(-15)), as well as in PLA2G6 on 22q13.1 (rs2284063, combined P = 3.4 x 10(-8)). In addition, variants in these two loci showed association with melanoma risk in 3,131 melanoma cases from two independent studies, including rs10757257 at 9p21, combined P = 3.4 x 10(-8), OR = 1.23 (95% CI = 1.15-1.30) and rs132985 at 22q13.1, combined P = 2.6 x 10(-7), OR = 1.23 (95% CI = 1.15-1.30). This provides the first report of common variants associated to nevus number and demonstrates association of these variants with melanoma susceptibility.

Vitamin D receptor gene polymorphisms, serum 25-hydroxyvitamin D levels, and melanoma: UK case-control comparisons and a meta-analysis of published VDR data.

We have carried out melanoma case-control comparisons for six vitamin D receptor (VDR) gene single nucleotide polymorphisms (SNPs) and serum 25-hydroxyvitamin D(3) levels in order to investigate the role of vitamin D in melanoma susceptibility. There was no significant evidence of an association between any VDR SNP and risk in 1028 population-ascertained cases and 402 controls from Leeds, UK. In a second Leeds case-control study (299 cases and 560 controls) the FokI T allele was associated with increased melanoma risk (odds ratio (OR) 1.42, 95% confidence interval (CI) 1.06-1.91, p=0.02). In a meta-analysis in conjunction with published data from other smaller data sets (total 3769 cases and 3636 controls), the FokI T allele was associated with increased melanoma risk (OR 1.19, 95% CI 1.05-1.35), and the BsmI A allele was associated with a reduced risk (OR 0.81, 95% CI 0.72-0.92), in each instance under a parsimonious dominant model. In the first Leeds case-control comparison cases were more likely to have a higher body mass index (BMI) than controls (p=0.007 for linear trend). There was no evidence of a case-control difference in serum 25-hydroxyvitamin D(3) levels. In 1043 incident cases from the first Leeds case-control study, a single estimation of serum 25-hydroxyvitamin D(3) level taken at recruitment was inversely correlated with Breslow thickness (p=0.03 for linear trend). These data provide evidence to support the view that vitamin D and VDR may have a small but potentially important role in melanoma susceptibility, and putatively a greater role in disease progression.

Sun-protective behaviors in families at increased risk of melanoma.

The aim of this study was to compare reported behavior in the sun in melanoma families with that of geographical healthy controls and to determine the predictors of that behavior to inform the process of counseling melanoma families. One hundred and seventy individuals with a family history of melanoma and 140 controls completed a postal questionnaire. Thirty-one percent of relatives reported sunburn in the previous summer, compared with 41% of controls. Fifty-five percent of relatives had acquired a suntan so that adherence to health education advice was disappointing. Male relatives were particularly likely to report sunburn. Higher knowledge scores correlated well with greater belief in ability to prevent melanoma, less desire for a tan, and more protective behaviors in relatives only (not in controls). We have shown that some psychological characteristics, sex, and age have an effect on behavior, so that the educational approaches needed will vary. "Better" behaviors were reported by melanoma cases than other relatives and by members of families with larger numbers of cases, which suggests that a belief that an individual is at particular risk of melanoma is important for compliance with preventive behaviors.

Prevalence of 9p21 deletions in UK melanoma families.

Although the CDKN2A gene has been shown to be the major genetic determinant governing high-penetrance susceptibility to melanoma, there remains a significant proportion of melanoma pedigrees in which germline mutations of CDKN2A have not been identified. We have therefore studied the prevalence of germline 9p deletions encompassing the CDKN2 locus in melanoma pedigrees, using multiplex ligation-dependent probe amplification. Germline deletions were found in 3 of 93 UK pedigrees, with no previously identified CDKN2A mutations. A hemizygous deletion of CDKN2A exon 1beta previously reported by this group was confirmed in one family and identified in a second. Microsatellite analysis determined that these two families were ancestrally related. In the third family, a novel p16 hemizygous deletion involving CDKN2A exons 1alpha, 2, and 3 was detected. An additional 9p21 deletion reported previously in a USA melanoma-neural system tumor family was shown to involve CDKN2A exon 1beta, and not p16. The CDKN2A exon 1beta deletions provide further evidence that this tumor suppressor gene is important in melanoma-neural system tumor susceptibility, but do not exclude the possibility of a novel gene or regulatory element also being deleted in this region. Deletions at 9p21 are rare and explain only a small proportion of melanoma susceptibility. This study is the first to comprehensively exclude deletions in melanoma-prone families with no previously identified CDKN2A mutations.

A network of investigator networks in human genome epidemiology.

The task of identifying genetic determinants for complex, multigenetic diseases is hampered by small studies, publication and reporting biases, and lack of common standards worldwide. The authors propose the creation of a network of networks that include groups of investigators collecting data for human genome epidemiology research. Twenty-three networks of investigators addressing specific diseases or research topics and representing several hundreds of teams have already joined this initiative. For each field, the authors are currently creating a core registry of teams already participating in the respective network. A wider international registry will include all other teams also working in the same field. Independent investigators are invited to join the registries and existing networks and to join forces in creating additional ones as needed. The network of networks aims to register these networks, teams, and investigators; be a resource for information about or connections to the many networks; offer methodological support; promote sound design and standardization of analytical practices; generate inclusive overviews of fields at large; facilitate rapid confirmation of findings; and avoid duplication of effort.