Smallest region of overlapping deletion in I p36 in human neuroblastoma: A I Mbp cosmid and PAC contig

In human neuroblastomas, the distal portion of Ip is frequently deleted, as if one or more tumor suppressor genes from this region were involved in neuroblastoma tumorigenesis. Earlier studies had identified a smallest region of overlapping deletion (SRO) spanning approximately 23 cM between the most distally retained DIS80 and by the proximally retained DIS244. In pursuit of generating a refined delineation of the minimally deleted region, we have analyzed 49 neuroblastomas of different stages for loss of heterozygosity (LOH) from Ipter to Ip35 by employing 26 simple sequence length polymorphisms. Fifteen of the 49 tumors (31%) had LOH; homozygous deletion was not detected. Seven tumors had LOH at all informative loci analyzed, and eight tumors showed a terminal or an interstitial allelic loss of Ip. One small terminal and one interstitial deletion defined a new 1.7 cM SRO, approximately I Mbp in physical length, deleted in all tumors between the retained DIS2731 (distal) and DIS2666 (proximal). To determine the genomic complexity of the deleted region shared among tumors, we assembled a physical map of the I Mbp SRO consisting predominantly of bacteriophage PI-derived artificial chromosome (PAC) clones. A total of 55 sequence-tagged site (STS) markers (23 published STSs and short tandem repeats and 32 newly identified STSs from the insert ends of PACs and cosmids) were assembled in a contig, resulting in a sequence-ready physical map with approximately one STS per 20 Kbp. Twelve genes (41BE, CD30, DFFA, DJI, DR3, FRAP, HKR3, MASP2, MTHFR, RIZ, TNR2, TP73) previously mapped to Ip36 are localized outside this SRO. On the basis of this study, they would be excluded as candidate genes for neuroblastoma tumorigenesis. Ten expressed sequence tags were integrated in the contig, of which five are Located outside the SRO. The other five from within the SRO may provide an entrance point for the cloning of candidate genes for neuroblastoma. (C) 2001 Wiley-Liss, Inc.