Deletion Mapping Suggests That the 1p22 Melanoma Susceptibility Gene Is a Tumor Suppressor Localized to a 9-Mb Interval Graeme J. Walker, 1 * James O. Indsto, 2 Raman Sood, 3 Mezbah U. Faruque, 3 Ping Hu, 3 Pam M. Pollock, 3 † Paul Duray, 4 Elizabeth A. Holland, 2 Kevin Brown, 3 † Richard F. Kefford, 2 Jeffrey M. Trent, 3 † Graham J. Mann, 2 and Nicholas K. Hayward 1 1 Human Genetics Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia 2 Westmead Institute for Cancer Research, University of Sydney, at Westmead Millennium Institute, Westmead, NSW, Australia 3 Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 4 Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland Loss of the short arm of chromosome 1 is frequently observed in many tumor types, including melanoma. We recently localized a third melanoma susceptibility locus to chromosome band 1p22. Critical recombinants in linked families localized the gene to a 15-Mb region between D1S430 and D1S2664. To map the locus more finely we have performed studies to assess allelic loss across the region in a panel of melanomas from 1p22-linked families, sporadic melanomas, and melanoma cell lines. Eighty percent of familial melanomas exhibited loss of heterozygosity (LOH) within the region, with a smallest region of overlapping deletions (SRO) of 9 Mb between D1S207 and D1S435. This high frequency of LOH makes it very likely that the susceptibility locus is a tumor suppressor. In sporadic tumors, four SROs were defined. SRO1 and SRO2 map within the critical recombinant and familial tumor region, indicating that one or the other is likely to harbor the susceptibility gene. However, SRO3 may also be significant because it overlaps with the markers with the highest 2-point LOD score (D1S2776), part of the linkage recombinant region, and the critical region defined in mesothelioma. The candidate genes PRKCL2 and GTF2B, within SRO2, and TGFBR3, CDC7, and EVI5, in a broad region encompassing SRO3, were screened in 1p22-linked melanoma kindreds, but no coding mutations were detected. Allelic loss in melanoma cell lines was significantly less frequent than in fresh tumors, indicating that this gene may not be involved late in progression, such as in overriding cellular senescence, necessary for the propagation of melanoma cells in culture. © 2004 Wiley-Liss, Inc. INTRODUCTION Nonrandom deletions affecting the short arm of chromosome 1 are the most common karyotypic abnormalities known to occur during the progres- sion from a normal melanocyte to a malignant mel- anoma cell (Limon et al., 1988; Smedley et al., 2000). We recently completed a genomewide scan for linkage to melanoma (Gillanders et al., 2003) using a panel of families not carrying mutations in the two known melanoma susceptibility genes, CDKN2A and CDK4. We localized a novel suscep- tibility locus to chromosome band 1p22. When families with the earliest age of onset of melanoma were selected, a maximum parametric LOD score of 4.65 (= 0) was obtained for marker D1S2779. Recombinants within the early-onset families de- lineated a 20-cM region between markers D1S2664 and D1S430. This region contains several candi- date genes, including PRKCL2, GTF2B, TGFBR3, CDC7, and EVI5, which map close to the marker with the peak LOD score (D1S2779). To date, most studies assessing loss of heterozy- gosity (LOH) on chromosome arm 1p in melanoma have examined only the telomeric region at 1p36. In the earliest report (Dracopoli et al., 1989), loss of alleles for markers on 1p was detected in 43% of melanoma biopsies and 52% of cell lines. Subse- quent studies found a relatively low rate of allelic loss within the 1p36 region in melanomas, ranging from 13% (Maitra et al., 2002) to 16% (Bogdan et al., 2001) and 22% (Walker et al., 1995). Deletions of the 1p36 region are also prevalent in other tu- mors (Bello et al., 2000; Benn et al., 2000; Mora et al., 2000; Sun et al., 2001), including pheochromo- cytomas, parathyroid adenomas, hepatocellular car- Supported by: NSW Cancer Council; National Health and Med- ical Research Council of Australia; National Institutes of Health. *Correspondence to: Graeme Walker, Queensland Institute of Medical Research, 300 Herston Rd, Herston, 4006, Queensland, Australia. E-mail: graemeW@qimr.edu.au †Current address: Translational Genomics Research Institute, Phoenix, AZ Received 1 December 2003; Accepted 5 April 2004 DOI 10.1002/gcc.20056 Published online 19 May 2004 in Wiley InterScience (www.interscience.wiley.com). GENES, CHROMOSOMES & CANCER 41:56 – 64 (2004) © 2004 Wiley-Liss, Inc.