Polymorphisms in the H19 Gene and the Risk of Bladder Cancer

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Polymorphisms in the H19 Gene and the Risk of Bladder Cancer Gerald W. Verhaegh, Linda Verkleij, Sita H.H.M. Vermeulen, Martin den Heijer, J. Alfred Witjes, Lambertus A. Kiemeney European Urology Volume 54, Issue 5, Pages 1118-1126 (November 2008) DOI: 10.1016/j.eururo.2008.01.060 Copyright © 2008 European Association of Urology Terms and Conditions

Fig. 1 Overview of selected tagging single nucleotide polymorphisms (tagSNPs) and their characteristics. (A) Location of the 18 SNPs within the H19 gene (5 exons) and 6-kb upstream region with a minor allele frequency>5% (HapMap genome browser B35, Chr11:1972982..1981641); DMR, differentially methylated region. The five tagSNPs that were selected are indicated by boxes. An LD-plot of the 18 SNPs in the 8.66-kb region is displayed by using r2-color scheme; black represents very high LD (r2=1), and white indicates the absence of correlation (r2=0) between SNPs. (B) The five tagSNPs and SNPs that are indirectly measured by them are listed with corresponding r2 values. Only rs217727 did not have a strong correlation with other SNPs. Major and minor alleles of the selected tagSNPs are given with their frequencies, based on the HapMap data for the CEU population. European Urology 2008 54, 1118-1126DOI: (10.1016/j.eururo.2008.01.060) Copyright © 2008 European Association of Urology Terms and Conditions

Fig. 2 H19 genotype analysis. (A) Schematic overview of the polymerase chain reaction (PCR) fragments containing the single nucleotide polymorphisms (SNPs) (indicated by diabolo symbols). Restriction sites and product sizes after digestion are indicated. (B) Restriction fragment length polymorphism (RFLP) analysis of the SNP-containing PCR fragments using the indicated restriction enzymes. M, DNA size marker; total, total PCR product before digestion. Note: For rs17658052, genotype AA was not found in this study; for rs217727, fragments smaller than 60bp are not shown. European Urology 2008 54, 1118-1126DOI: (10.1016/j.eururo.2008.01.060) Copyright © 2008 European Association of Urology Terms and Conditions

Fig. 3 Folding of the H19 RNA. (A) Secondary structure of the H19 RNA (GenBank accession no.: NR_002196). Encircled are the regions containing single nucleotide polymorphisms (SNPs) rs2839698 and rs217727. (B) Structure of H19 containing the C allele of rs2839698 at position 213 (the RNA containing the T allele of rs2839698 adopts an identical conformation; not shown). (C and D) Structure of H19 containing the T and C allele, respectively, of rs217727 at position 1806. The solid arrows indicate the position of the SNPs. All structures were predicted with Mfold software (version 3.1.2; http://bioweb.pasteur.fr). European Urology 2008 54, 1118-1126DOI: (10.1016/j.eururo.2008.01.060) Copyright © 2008 European Association of Urology Terms and Conditions