Cloning and Mapping of Human Chromosome 6q26–q27 Deleted in B-Cell Non-Hodgkin Lymphoma and Multiple Tumor Types

• Published in: Genomics (San Diego, Calif.) Vol. 50; no. 2; pp. 170 - 186
• Main Authors: Hauptschein, Robert S., Gamberi, Barbara, Rao, Pulivarthi H., Frigeri, Ferdinando, Scotto, Luigi, Venkatraj, V.S., Gaidano, Gianluca, Rutner, Torin, Edwards, Yvonne H., Chaganti, R.S.K., Dalla-Favera, Riccardo
• Format: Journal Article
• Language: English
• Published: San Diego, CA Elsevier Inc 01-06-1998; Elsevier
• Subjects: Biological and medical sciences; Chromosome Deletion; Chromosome Mapping; Chromosomes, Artificial, Yeast; Chromosomes, Human, Pair 6; Cloning, Molecular; Electrophoresis, Gel, Pulsed-Field; Genes, Tumor Suppressor - genetics; Hematologic and hematopoietic diseases; Humans; In Situ Hybridization, Fluorescence; Kinesin - genetics; Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis; Loss of Heterozygosity; Lymphoma, B-Cell - genetics; Medical sciences; Minisatellite Repeats; Molecular Probe Techniques; Mutation; Myosins - genetics; Neoplasms - genetics; Polymorphism, Restriction Fragment Length; Sequence Tagged Sites; Genetic mapping; Human; Malignant hemopathy; B-Lymphocyte; Chromosome C6; Non Hodgkin lymphoma; Contig; Lymphoproliferative syndrome; Loss of heterozygosity; Deletion; Tumor; Mutation; Physical map; Tumor suppressor gene
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1006/geno.1998.5321

Frequent deletions of the distal region on the long arm of chromosome 6 have been reported in multiple human tumors including B-cell non-Hodgkin lymphoma (B-NHL), suggesting the presence of one or more tumor suppressor genes (TSGs) at this locus. Previously, we identified a region of minimal molecular deletion at 6q25–q27 (RMD-1) in B-NHL cases. To facilitate positional cloning efforts to identify the RMD-1 TSG(s), a yeast artificial chromosome (YAC) contig consisting of 110 clones was constructed across 6q26–q27 by sequence-tagged site/probe contentmapping. The contig integrates 79 ordered markers including restriction fragment length polymorphisms, minisatellites, microsatellites, YAC-insert termini, expressed sequence tags, and known genes. It spans 34 cM and has a minimal tiling path of approximately 12 clones, covering an estimated 9–14 Mb with nearly every marker on the map showing at least double linkage to its adjacent markers. Dual-color fluorescencein situhybridization of selected marker pairs on normal pachytene chromosome 6 further confirmed the YAC-based mappings. Utilizing a loss of constitutional heterozygosity assay in the B-NHL tumor panel, 24 additional 6q26–q27 polymorphic markers (21 mapping to the contig) further defined RMD-1 between markers D6S186 proximally and D6S227 distally. The minimal tiling path of the B-NHL RMD-1 consists of approximately 8 YAC clones, providing a size estimate of 5–9 Mb. This interval contains, in their entirety, several smaller candidate TSG critical regions previously delimited in other tumor systems. The AF-6 gene, mapping within RMD-1, revealed no mutations in a small subset of B-NHL. The deletion and physical maps presented herein provide a framework for the identification of the gene(s) involved in B-NHL as well as other malignancies and diseases mapped to this region and provide the initial reagents for large-scale genomic sequencing.