Vol. 9, Issue 3, 226-233, March 1999

Identification and Characterization of a Homozygous Deletion Found in Ovarian Ascites by Representational Difference Analysis

¹ Imperial Cancer Research Fund (ICRF) Medical Oncology Unit and ² Medical Research Council Human Genetics Unit (MRC HGU), Western General Hospital, Edinburgh EH4 2XU, Scotland

We have performed representational difference analysis (RDA) on DNA from tumor cells and normal fibroblasts isolated from the ascites of a patient with ovarian cancer. Five of six products of the RDA were homozygously deleted from the tumor DNA. One of these products has been characterized and identifies a homozygous deletion of ~6.9 Mb at chromosome 9p21 in the original ovarian tumor material. This deletion encompasses CDKN2A (p16), CDKN2B (p15), and IFN-. PCR analysis of other tumor cell lines using the novel STS based on the RDA product has shown it to lie between IFN- and p16, and to identify the distal extent of a homozygous deletion in another ovarian cancer cell line. These data provide further evidence for a tumor suppressor locus distinct from, but mapping close to, p16 on 9p21. Cytogenetic analysis using comparative genomic hybridization (CGH) performed on the same primary tumor confirmed a loss of material from chromosome 9p. However, the CGH technique had neither the resolution nor the sensitivity to define a subregion of homozygous loss.

[The GenBank accession no. for this sequence is AF113912.]