Fine Mapping of a Tumour Suppressor Candidate Gene Region in 1p36.2-3, Commonly Deleted in Neuroblastomas and Germ Cell Tumours Katarina Ejeska ¨r, PhD, 1 Rose-Marie Sjo ¨ berg, BMA, 1 Frida Abel, BSc 1 Per Kogner, MD, PhD, 2 Peter F. Ambros, PhD, 3 and Tommy Martinsson, PhD 1* Background. A common genetic feature of neuroblastomas, which is also an important prognostic factor, is deletion of chromosome region 1p. The deletion of 1p often involves a deletion of varying size, with a consensus re- gion within the most distal bands 1p36.2-3. The neuroblastoma SRO (shortest region of overlap of deletions) presented earlier by our group was defined distally by the cluster of loci D1S80/ D1Z2/CDC2L1 and proximally by loci D1S244, i.e., approximately 25 cM. The 1p de- letions are, however, not restricted to neuro- blastoma tumours. In fact, a large spectrum of tumour types display deletions to varying de- grees of 1p. Procedure. We have exploited the possibility of using deletions of other tumour types, preferentially that of germ cell tumours, and combining the deletions with that of the neuroblastoma SRO. Also in germ cell tumours, distal 1p-deletions have been shown to have prognostic significance. Results. We found in our germ cell tumours a SRO ranging from D1S508 to D1S200. Interestingly, this region only partially overlapped (approximately 5 cm) with our neuroblastoma SRO in region D1S508 to D1S244. We have thus focused on analysing this smaller region in the search for genes in- volved in the genesis of different cancers. We have performed radiation hybrid mapping of a large number of markers, STSs, ESTs, and others known to reside in 1p. We have also initiated the development of a BAC contig of the region. FISH, and fibre-FISH mapping of BACs were also performed. Conclusions. The data pre- sented here constitute an ongoing work with the aim of identifying and cloning gene(s) im- portant for development of germ cell tumours, neuroblastomas, and possibly other tumours. Med. Pediatr. Oncol. 36:61–66, 2001. © 2001 Wiley-Liss, Inc. Key words: neuroblastoma; 1p-deletion; tumor supressor gene INTRODUCTION Neuroblastoma is a childhood tumour derived from the neural crest. Common genetic features, which are also important prognostic factors, are deletions of chro- mosome region 1p and MYCN-amplification. The dele- tion of 1p has been characterised by us and others with different techniques, e.g., cytogenetic analysis [1– 4], in situ hybridisation, FISH (fluorescence in situ hybridisa- tion) techniques [5,6], and by detection of loss of het- erozygosity (LOH) [7–10]. The deletion of 1p often in- volves a large proportion of the distal region of the short arm, but some tumours and cell lines display smaller deletions, involving only regions in 1p36 [4,7,8,10–14]. Thus, this region is a candidate position for harbouring one or more neuroblastoma tumour suppressor (NBS) gene(s). There is additional support for a NBS gene in 1p36 in two neuroblastoma cases carrying constitutional aberrations in the 1p36 region [15,16]. In order to loca- lise, and ultimately to clone the NBS gene, several groups, including ours, have been trying to define the smallest region of overlap (SRO) of deletions in neuro- blastoma cases. The most informative neuroblastoma SRO published so far is by our group [10,14] where the SRO is defined distally by the cluster of loci D1S80/ D1Z2/CDC2L1, and proximally by loci D1S244. This region is approximately 25 cm using available maps [17]. The large size of the region has hampered efforts to isolate the gene by the conventional positional cloning methods. We have, to date, analysed approximately 125 neuro- blastoma tumours, most of Swedish origin [10, and un- published data], and approximately 26% of unselected primary tumours have deletions involving 1p. This figure is considerably higher for advanced stages of tumours, i.e., approximately 60–70% of stage 3–4 tumours. The deletions are, however, often large, generally involving the region 1p32-1pter. With regard to the detailed loca- tion of the NBS gene, there have been no cases giving more information than that reported by us [14]. 1 Department of Clinical Genetics, Sahlgrenska University Hospital/ East, Gothenburg, Sweden 2 Woman and Child Health, Childhood Cancer Research Unit, Karo- linska Institute, Karolinska Hospital, Stockholm, Sweden 3 CCRI, St. Anna Kinderspital, Vienna, Austria Grant sponsor: Swedish Cancer Society; Grant sponsor: Children’s Cancer Foundation; Grant sponsor: King Gustav V Jubilee Clinic Can- cer Research Foundation; Grant sponsor: Assar Gabrielsson Founda- tion. *Correspondence to: T. Martinsson, Department of Clinical Genetics, Sahlgrenska University Hospital /East, S-416 85 Gothenburg, Sweden. E-mail: Tommy.Martinsson@clingen.gu.se Medical and Pediatric Oncology 36:61–66 (2001) © 2001 Wiley-Liss, Inc.