1. ¹Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
2. ²Department of Biomathematics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
3. ³Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
4. ⁴University of Texas Southwestern Medical Center, Dallas, TX, USA
5. ⁵Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
6. ⁶Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA

Correspondence: Dr B Czerniak, MD, PhD, Department of Pathology, The University of Texas MD Anderson Cancer Center, Box 085, 1515 Holcombe Boulevard, Houston, TX 77030, USA. E-mail: bczernia@mdanderson.org

^*These authors contributed equally to this study

Received 12 October 2005; Revised 11 November 2005; Accepted 12 November 2005; Published online 9 January 2006.

Abstract

In this paper, we present whole-organ histologic and genetic mapping studies using hypervariable DNA markers on chromosome 13 and then integrate the recombination- and single-nucleotide polymorphic sites (SNPs)-based deletion maps with the annotated genome sequence. Using bladders resected from patients with invasive urothelial carcinoma, we studied allelic patterns of 40 microsatellite markers mapping to all regions of chromosome 13 and 79 SNPs located within the 13q14 region containing the RB1 gene. A whole-organ histologic and genetic mapping strategy was used to identify the evolution of allelic losses on chromosome 13 during the progression of bladder neoplasia. Markers mapping to chromosomal regions involved in clonal expansion of preneoplastic intraurothelial lesions were subsequently tested in 25 tumors and 21 voided urine samples of patients with bladder cancer. Four clusters of allelic losses mapping to distinct regions of chromosome 13 were identified. Markers mapping to the 13q14 region that is flanked by D13S263 and D13S276, which contains the RB1 gene, showed allelic losses associated with early clonal expansion of intraurothelial neoplasia. Such losses could be identified in approximately 32% bladder tumor tissue samples and 38% of voided urines from patients with bladder cancer. The integration of distribution patterns of clonal allelic losses revealed by the microsatellite markers with those obtained by genotyping of SNPs disclosed that the loss within an approximately 4-Mb segment centered around RB1 may represent an incipient event in bladder neoplasia. However, the inactivation of RB1 occurred later and was associated with the onset of severe dysplasia/carcinoma in situ. Our studies provide evidence for the presence of critical alternative candidate genes mapping to the 13q14 region that are involved in clonal expansion of neoplasia within the bladder antecedent to the inactivation of the RB1 gene.