Figure 11

Map of LOP within 3.16-Mb segment around RB1. (a) Allelic losses were tested on 111 paired samples of bladder tumors and peripheral blood using SNP multiplex technology. Predicted sizes of LOP are depicted as blue bars and a continuous red line shows their frequency. The genomic map above the diagram shows positions of individual genes (solid black bars) and tested SNPs (thin black downward bars). Our previously published data were based on mapping of 84 paired samples of bladder tumor and peripheral blood DNA with 100 SNPs. The selected SNPs were located primarily inside and around the known and predicted genes within the tested region with a mapping gap centromeric to RB1 between the genes HTR2A and SUCLA2. The absence of SNPs spanning a long segment centromeric to RB1 might have resulted in an artificial shift of the deletion frequency curve telomeric to RB1. To address this concern, we tested additional eight SNPs spanning a gap between HTR2A and SUCLA2 and increased the number of tested paired bladder tumor and non-tumor DNA samples to 111. The pattern and frequency of allelic loss generated by this approach were almost identical to our previously data¹⁶ and implies that the most frequent breakpoint is located between RCBTB2 and CDADC1. Overall, the pattern of allelic losses suggests the presence of additional candidate FR genes mapping telomerically to RB1. (b) The allelic losses are related to histologic grade, RB protein expression, RB1 mutation, methylation of ITM2B, and nucleotide substitutions of P2RY5, as summarized in the diagram on the right. Details of RB1 sequencing were published previously.¹⁶ L, low grade (grade 1–2); H, high grade (grade 3); solid blue dots indicate the absence of RB protein expression, mutation of RB1, methylation of ITM2B, and nucleotide substitutions in P2RY5. Red crosses indicate tests not performed. (c) Putative NAHR regions identified by the presence of similar sequences in the same orientation using Human Chained Self Alignment browser. (d) Recombination rates based on HapMap. (e) Recombination rate based on Perlegen. (f) Alu repeat content per 10-kb windows. (g) Human-specific retrotransposons based on UCSC Alignment Nets. (h) Human polymorphic structural variants based on the Center for Applied Genomics Database of Genomic Variants and the UCSC Structural Var track. (i) Placental mammal conservation scores in 500-bp windows. (j) Most conserved elements, 28-way vertebrate Multiz alignment.