Discrete Breakpoint Mapping and Shortest Region of Overlap of Chromosome Arm 1q Gain and 1p Loss in Human Hepatocellular Carcinoma Detected by Semiquantitative Microsatellite Analysis Takafumi Nishimura, 1 Naoshi Nishida, 1* Teruaki Itoh, 1 Toshiki Komeda, 1 Yoshihiro Fukuda, 2 Iwao Ikai, 3 Yoshio Yamaoka, 4 and Kazuwa Nakao 1 1 Department of Medicine and Clinical Science, Kyoto University Graduate School of Medicine, Kyoto, Japan 2 School of Health Science, Faculty of Medicine, Kyoto University, Kyoto, Japan 3 Department of Gastroenterological Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan 4 Kitano Hospital, Osaka, Japan Recurrent chromosomal gain at 1q is one of the most common features of human hepatocellular carcinoma (HCC), but how the gain at 1q contributes to hepatocarcinogenesis is still unclear. To identify the target genes, precise determination of the shortest region of overlap (SRO) and of breakpoints is necessary. Similarly, the role of loss at 1p, which is also a major cytogenetic aberration in HCC, needs to be determined. Fifty HCCs were examined with the aid of 59 microsatellite markers distributed throughout both arms of chromosome 1. To detect allelic gain effectively, the cutoff value of the allelic imbalance index was set at 0.70. Alleles showing imbalance were subjected to multiplex PCR, using a retained allele as an internal control, to determine whether the imbalance was the result of chromosomal gain or loss. The SRO of the gains was defined as D1S2878–D1S2619 (1q23.– q25.3, 16.9 Mb), which involved 36 cases (72%). Gains in the number of copies of certain oncogenes within this region seemed to be critical for the pathogenesis of HCC. In contrast, the centromeric breakpoints of these gains varied, but they tended to occur mainly in the pericentromeric region (26 of 50 cases, 52%). Rearrangement of specific genes associated with the gains is unlikely. On the other hand, the SRO of deletion was defined as D1S2893–D1S450 (1p36.32–p36.22, 5.1 Mb). Four known putative tumor-suppressor genes (TP73, RIZ1, NBL1/DAN, and CDKN2C) were outside the SRO, suggesting the presence of other candidate genes with critical roles in hepatocarcinogenesis. © 2004 Wiley-Liss, Inc. INTRODUCTION A growing number of recent cytogenetic analy- ses, using techniques such as comparative genomic hybridization (CGH) or spectral karyotyping (SKY), have demonstrated that gains or losses in certain chromosomal regions are common features of malignant cells. In hepatocellular carcinoma (HCC), recurrent chromosomal alterations such as -1p, +1q, -4q, +6p, -6q, -8p, +8q, -13q, -16q, -17p, and +17q have been reported (Mar- chio et al., 1997; Kusano et al., 1999; Lin et al., 1999; Qin et al., 1999; Sakakura et al., 1999; Wong et al., 1999; Chen et al., 2000; Marchio et al., 2000; Tomillo et al., 2000; Wong et al., 2000; Balsara et al., 2001; Collonge-Rame et al., 2001; Niketeghad et al., 2001; Shiraishi et al., 2001; Wang et al., 2001; reviewed in Nishida et al., 2003), but their specific role in hepatocarcinogenesis is still unclear. Of these alterations, the gain at 1q is one of the most frequent chromosomal aberrations in HCC (de- tected in 60% of HCCs on average), so clarification of its impact on hepatocarcinogenesis is necessary. The function of gross chromosomal gain, other than high-copy amplification of limited regions of chromosomes, generally remains unclear. How- ever, the following two scenarios are considered possible. First, an increase in the number of copies of a gene may result in an increase in the expres- sion of the gene (Virtaneva et al., 2001). If an increase of specific genes is crucial for carcinogen- esis, the shortest region of overlap (SRO) may con- centrate on these genes. Second, the results of a few studies that combined CGH and SKY sug- gested that chromosomal gain may result from un- balanced translocation (Pang et al., 2000; Tsushimi et al., 2001). If a fusion protein plays an important *Correspondence to: Naoshi Nishida, Department of Medicine and Clinical Science, Kyoto University Graduate School of Medi- cine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan. E-mail: naoshi@kuhp.kyoto-u.ac.jp Received 25 November 2003; Accepted 27 August 2004 DOI 10.1002/gcc.20117 Published online 19 October 2004 in Wiley InterScience (www.interscience.wiley.com). GENES, CHROMOSOMES & CANCER 42:34 – 43 (2005) © 2004 Wiley-Liss, Inc.