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In the past few years high throughput methods for assessment of DNA copy number alterations have witnessed rapid progress. Both ‘in house’ developed BAC, cDNA, oligonucleotide and commercial arrays are now available and widely applied in the study of the human genome, particularly in the context of disease. Cancer cells are known to exhibit DNA losses, gains and amplifications affecting tumor suppressor genes and proto-oncogenes. Moreover, these patterns of genomic imbalances may be associated with particular tumor types or subtypes and may have prognostic value. Here we summarize recent array CGH findings in neuroblastoma, a pediatric tumor of the sympathetic nervous system. A total of 176 primary tumors and 53 cell lines have been analyzed on different platforms. Through these studies the genomic content and boundaries of deletions, gains and amplifications were characterized with unprecedented accuracy. Furthermore, in conjunction with cytogenetic findings, array CGH allows the mapping of breakpoints of unbalanced translocations at a very high resolution. Copyright © 2006 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Recently, the EXTL1 gene, a member of the EXT tumor suppressor gene family, has been mapped to 1p36, a chromosome region which is frequently implicated in a wide variety of malignancies, including breast carcinoma, colorectal cancer and neuroblastoma. In this study, we show that the EXTL1 gene is located between the genetic markers D1S511 and D1S234 within 200 kb of the LAP18 gene on chromosome 1p36.1, a region which has been proposed to harbor a tumor suppressor gene implicated in MYCN-amplified neuroblastomas. In addition, we determined the genomic structure of the EXTL1 gene, revealing that the EXTL1 coding sequence spans 11 exons within a 50-kb region. [ABSTRACT FROM AUTHOR]

This article describes an experiment on mapping of SHOX2 (alias OG12X and SHOT) to human chromosome bands 3q25 - q26.1 by Fluorescence in situ hybridization (FISH). The human SHOX2 (alias OG12X and SHOT) is a recently identified homeobox gene of which the mouse homologue is expressed during heart and craniofacial development. It was mapped to human chromosome 3q22 - q26 by radiation hybrid mapping and to 3q25 - q26 by FISH. The DNA of the PAC clones was prepared using an alkaline lysis miniprep method and labeled with biotin- 1 6-dUTP (0.4 mM, Boehringer) by nick translation.

This article describes the mapping of the cellular retinol-binding protein 1 gene (RBP1) and of the coatomer beta subunit gene (COPB2) to human chromosome band 3q23 by in situ hybridization. The human cellular retinol-binding protein 1 (RBP 1) is responsible for the intracellular transport of vitamin A to the final site of action. The DNA of the PAC clones was prepared using an alkaline lysis mini- prep method and labeled with digoxigenin-1 1-dUTP (0.4 mM, Boehringer) by nick translation. The PACs were cohybridized with a biotinylated probe for the centromeric region of chromosome 3.