Genome-wide semiquantitative microsatellite analysis of human hepatocellular carcinoma: discrete mapping of smallest region of overlap of recurrent chromosomal gains and losses

Recurrent chromosomal gains at 1q, 6p, 8q, and 17q, or losses at 1p, 4q, 6q, 8p, 9p, 13q, 16q, and 17p are common features of human hepatocellular carcinoma (HCC). For precise determination of the shortest region of overlap (SRO), 49 HCC obtained at the time of surgery or autopsy were subjected to comprehensive microsatellite analysis by using 400 markers distributed at almost equal distances throughout the 22 autosomes and X chromosomes. Each allele showing imbalance was subjected to comparative duplex polymerase chain reaction using a retained allele as an internal control to determine whether the imbalance was the result of chromosomal gain or loss. The following SRO of recurrent chromosomal gains and losses were determined: −1p36.22∼p36.33, D1S450-D1S2893, 5.0 mega–base pairs (Mbp); +1q23.3∼q25.3, D1S2878-D1S2619, 16.9 Mbp; −4q21.2∼q24, D4S2964-D4S1572, 23.0 Mbp; −6q23.3∼qter, D6S292-qter, 34.7 Mb; −8p22∼p23.1, D8S549-D8S550, 4.8 Mbp; +8q12.2∼q24.13, D8S260-D8S514, 61.8 Mbp; −13q13.3∼q22.1, D13S218-D13S156, 35.6 Mbp; −16q22.1∼qter, D16S503-qter, 26.7 Mbp; and −17p12∼pter, D17S921-pter, 14.2 Mbp. Contrary to our initial expectations, many HCC showed major deletions or additions of chromosome arms, so that a number of genes were included in the SRO. Although some putative oncogenes or tumor suppressor genes mapped in these SRO may be important, relative copy number changes of numerous other genes may affect pathogenesis of HCC.