Phylogenetic Trees for <i>VEGF</i> Haplotypes and Association with Bladder Cancer Risk among 926 Cases and 900 Controls with DNA in the iPLEX Assay, Spanish Bladder Cancer Study

<div><p>See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030029#pgen-0030029-g001" target="_blank">Figure 1</a> for block definitions. Of the 29 <i>VEGF</i> SNPs determined, two had low genotypic variation in our population; therefore, haplotype analyses were based on the remaining 27 SNPs. Polymorphic bases are in 5′ to 3′ order: Block 1(<b>rs833052</b> and rs866236); Block 2 (<b>rs1109324</b>, <b>rs1547651</b>, rs833060, rs699947, rs1005230, rs833061, rs1570360, rs2010963, <b>rs25648</b>, rs833067, rs3025042, rs833068, <b>rs3024994</b>, rs735286, rs3024998, rs3025000, and rs3025006); and Block 3 (rs3025030, rs3025033, rs3025035, and rs3025036). Bolded rs numbers are for individual SNPs significantly associated with bladder cancer risk.</p><p>Eleven cases and 13 controls with missing data on more than 15 of the 17 SNPs in Block 2 were excluded from haplotype analyses because their inclusion resulted in lack of convergence. Nucleotide changes significantly associated with risk in the individual genotype analyses are shown in boxes. The most common haplotye is the reference category. Haplotypes with the common variant for each individual SNP are CC for Block 1, GAGCCGTGCTGGCCCCC for Block 2, and GACC for Block 3.</p></div

Gene Map and LD Plot of <i>VEGF</i> Gene

<p>Color scheme is based on D′ and logarithm of the odds of linkage (LOD) score values: white D′ < 1 and LOD < 2, blue D′ = 1 and LOD < 2, shades of pink/red: D′ < 1 and LOD ≥ 2, and bright red D′ = 1 and LOD ≥ 2. Numbers in squares are D′ values (values of 1.0 are not shown). Block definition is based on the Gabriel et al. method [34]. Two (rs3024989 and rs367173) of the 29 SNPs determined are not shown because of low variation in this population. Red rectangles in the gene map represent exons.</p

A Scale Map of the 26 SNPs Genotyped in the MEC Screening Panel and a Plot of the Pattern of Linkage Disequilibrium among Them (in Whites)

<p>The four tag SNPs are markers with arrows, and the block of high linkage disequilibrium and limited haplotype diversity spanning <i>HSD17B1</i> is highlighted.</p