Cancer Genetics and Cytogenetics 160 (2005) 1–14 Lead article Molecular cytogenetic analysis of chromosomes 1 and 19 in glioma cell lines Mark E. Law a , Kristen L. Templeton a , Gaspar Kitange a , Justin Smith b , Anjan Misra c , Burt G. Feuerstein c , Robert B. Jenkins a, * a Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic and Foundation, 200 First Street SW, Rochester, MN 55905 b Department of Neurosurgery, c Department of Laboratory Medicine, University of California, San Francisco, CA Received 12 October 2004; received in revised form 16 November 2004; accepted 19 November 2004 Abstract Deletions of chromosome 1p and 19q arms are frequent genetic abnormalities in primary human gliomas and are especially common in oligodendrogliomas. However, the chromosome 1p and 19q status of many glioma cell lines has not been established. Using homozygosity mapping, fluorescence in situ hybridization (FISH), and comparative genomic hybridization to arrayed BAC (CGHa), we screened 17 glioma cell lines for chromosome 1 and 19 deletions. Sequence tagged site polymor- phisms were used to evaluate the cell lines for regions of chromosome 1p and 19q homozygosity. Cell lines A172, U251, TP265, U118, SW1088, U87, SW1783, and D32 contained significant regions of 19q homozygosity. In addition, A172, U87, TP483, D37, U118, MO67, and TP265 contained significant regions of 1p homozygosity. FISH probes localized to 1p36.32 and 19q13.33 as well as CGHa were used to determine which cell lines had deletions of 1p and/or 19q. Cell lines A172, U87, TP483, TP265, H4, U251, and D37 were deleted for portions of 1p. CGHa and homozygosity mapping of these cell lines define a 700-kilobase (Kb) common deletion region that is encompassed by a larger deletion region previously mapped in sporadic gliomas. This common deletion region is localized at 1p36.31 and includes CHD5, a putative tumor suppressor gene. Cell line A172 was observed to have a deletion between 19q13.33 and 19q13.41, while U87 was observed to have a smaller deletion of 19q13.33. Cell lines A172 and U87 contain 1p and 19q deletions similar to those found in sporadic gliomas and will be useful cellular reagents for evaluating the function of putative 1p and 19q glioma tumor suppressor genes.  2005 Elsevier Inc. All rights reserved. 1. Introduction Chromosome 1p and 19q arm deletions are frequent ge- netic abnormalities in primary gliomas, especially oligoden- drogliomas. While 1p deletions are relatively common in other types of tumors, 19q deletions appear to be common only in gliomas [1]. Oligodendrogliomas with deletion of chromosome arms 1p and/or 19q have been reported to have a better survival and response to radiation therapy and chemotherapy [2–4]. Minimal deletion regions on 1p and 19q have been mapped recently using primary glioma specimens [5,6]. A comprehensive analysis of 1p and 19q alterations, however, had not been performed on the existing glioma cell lines. * Corresponding author. Tel.: (507) 284-9617; fax: (507) 284-0043. E-mail address: rjenkins@mayo.edu (R.B. Jenkins). 0165-4608/05/$ – see front matter  2005 Elsevier Inc. All rights reserved. doi:10.1016/j.cancergencyto.2004.11.012 The observation that 1p and 19q deletions are frequent in gliomas suggests that these two chromosomes may harbor genes responsible for the suppression of these tumors. De- spite the ongoing effort in positional cloning, no credible can- didate gene has yet been discovered. Thus, mapping 1p and 19q deletions in glioma cell lines may be a necessary step toward isolating these putative tumor suppressor genes. For example, the cloning of CDKN2A (and its relatives) and PTEN was facilitated by finding cell lines with loss of these specific regions, adding chromosomal material, and mapping revertants [7,8]. In addition, cell lines with deletions may be useful cellular reagents for functional studies of putative tumor suppressor genes. We used several approaches to identify chromosome 1p and 19q alterations in glioma cell lines, including loss of heterozygosity (LOH), also referred to herein as homozygos- ity mapping [9], multicolor fluorescence in situ hybridization