Human Molecular Genetics Advance Access published online on January 24, 2009
Human Molecular Genetics, doi:10.1093/hmg/ddp046
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Germline CDH1 Deletions in Hereditary Diffuse Gastric Cancer Families
1 Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal 2 Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal 3 Hereditary Cancer Program, British Columbia Cancer Agency, Vancouver V5Z 4E6, Canada 4 CBM S.c.r.l., AREA Science Park, Basovizza, 34012 Trieste, Italy 5 Prostate Centre Microarray Facility, Vancouver V6H 3Z6, Canada 6 Department of Human Pathology and Oncology, Section of Surgical Oncology, Translational Research Laboratory, University of Siena, 53100 Siena, Istituto Toscano Tumori (ITT), Italy 7 Division of Surgical Oncology, University of Siena, 53100 Siena, Italy 8 MRC Holland, 1057 DN Amsterdam, The Netherlands 9 MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge CB2 0XZ, UK 10 Department of Surgery, Technische Universität München, 81675 Munich, Germany 11 Institute of Pathology, Technische Universität München, D-81675 Munich, Germany 12 Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, UK 13 Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK 14 Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul 151-742, South Korea 15 Departments of Surgery and Medical Genetics, Henry Ford Hospital, Detroit, MI 48202, USA
* Correspondence to: David Huntsman Phone:+1 604 877-6000 [2148] Fax:+1 604 877-6178 Email: dhuntsma{at}bccancer.bc.ca
Received December 23, 2008; Revised January 21, 2009; Accepted January 22, 2009
Germline point or small frameshift CDH1 mutations were identified in 30-50% of hereditary diffuse gastric cancer (HDGC) families. We hypothesized that CDH1 genomic rearrangements would be found in HDGC and identified 160 families with either two gastric cancers in first-degree relatives, with at least one diffuse gastric cancer (DGC) diagnosed before age 50, or three or more DGC in close relatives diagnosed at any age. Sixty-seven carried CDH1 mutations. We screened germline DNA from 93 mutation negative probands for large genomic rearrangements by Multiplex Ligation-Dependent Probe Amplification (MLPA). Potential deletions were validated by RT-PCR and breakpoints cloned using a combination of oligo-CGH-arrays and long-range-PCR. In-silico analysis of CDH1 locus was used to determine a potential mechanism for these rearrangements. Six of 93 (6.5%) previously described mutation negative HDGC probands, from low GC incidence populations, carried genomic deletions (UK and North America). Two families carried an identical deletion spanning 193,593bps, encompassing the full CDH3 sequence and CDH1 exons 1 and 2. Other deletions affecting exons 1, 2, 15 and/or 16 were identified. The statistically significant over-representation of Alus around breakpoints indicates it as a likely mechanism for these deletions. When all mutations and deletions are considered, the overall frequency of CDH1 alterations in HDGC is approximately 46% (73/160). CDH1 large deletions occur in 4% of HDGC families by mechanisms involving mainly non-allelic homologous recombination in Alu repeat sequences. As the finding of pathogenic CDH1 mutations is useful for management of HDGC families, screening for deletions should be offered to at risk families.