pcmr12130-sup-0001-FigureS1.tifimage/tif78KFigure S1. Schematic illustration of genomic structure of PAX3 and location of genotyped SNPs.
pcmr12130-sup-0002-FigureS2a.tifimage/tif217KFigure S2. (A) rs6754024, (B) rs6436309, (C) rs1549773, (D) rs13410020. A, B, C, and D plots were generated using the Genvar web tool (SNP–gene association analysis) and published expression data from Nica et al., 2011. The results reported are from eQTL data of Twins dataset of MuTHER study. The Twins pairs were separated in two unrelated groups. The individuals are plotted on stripcharts. The four panels showed the results of the correlation between PAX3 SNP and PAX3 transcript levels in three different tissues, examined using Spearman. The observed and permutation P-values are shown for each analysis. The four PAX3 SNPs minor alleles were correlated with decreased PAX3 gene expression. The SNP rs6754024, the only genotyped, has been associated with high nevus number in melanoma cases from BCN and Leeds. The SNP rs6436309 is in linkage (r2 = 0.53) with rs6754024. The SNPs rs1549773 (r2 = 1) and rs13410020 (r2 = 0.68) are in LD with rs2855268; this SNP has been found to protect from high nevus number in BCN melanoma cases and TwinsUK. A = adipose tissue biopsy (n = 160), L = lymphoblastoid cell lines (n = 166), S = skin tissue biopsy (n = 160), eQTL = expression quantitative trait loci, Twin1 = unrelated twin group 1, Twin2 = unrelated twin group 2, rho = Spearman's rank correlation coefficient between genotype and transcript levels, P = P-value for correlation, Pemp = adjusted P-value by permutation test.
pcmr12130-sup-0006-TableS1.docWord document96KTable S1. (1.1) Genes selected in BCN study. (1.2) The 21 SNPs significantly associated with nevus number in BCN genotyping analysis.
pcmr12130-sup-0007-TableS2.docWord document132KTable S2. (2.1) Association between Pax3 SNPS and nevus number in controls from Leeds. (2.2) Nevus number analysis as continuous variable: association between PAX3 SNPs and nevus number in melanoma cases and controls from Leeds. (2.3) Significant associations between PAX3 SNPs and nevus number in singletons (half Twins UK population, n = 1494). (2.4) Clinical characteristic distribuition of melanoma cases with low and high nevus number from Barcelona. (2.5) clinical characteristic distribuition of controls and melanoma cases from leeds.

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