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Germline CDH1 deletions in hereditary diffuse gastric cancer families.

Oliveira C, Senz J, Kaurah P, Pinheiro H, Sanges R, Haegert A, Corso G, Schouten J, Fitzgerald R, Vogelsang H, Keller G, Dwerryhouse S, Grimmer D, Chin SF, Yang HK, Jackson CE, Seruca R, Roviello F, Stupka E, Caldas C, Huntsman D - Hum. Mol. Genet. (2009)

Bottom Line: The statistically significant over-representation of Alus around breakpoints indicates it as a likely mechanism for these deletions.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Pathology and Immunology, University of Porto, Portugal.

ABSTRACT
Germline CDH1 point or small frameshift mutations can be 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 and 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 germline CDH1 point or small frameshift mutations. We screened germline DNA from the 93 mutation negative probands for large genomic rearrangements by Multiplex Ligation-Dependent Probe Amplification. 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 the 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 (UK and North America), carried genomic deletions (UK and North America). Two families carried an identical deletion spanning 193 593 bp, 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.

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MLPA output from the six HDGC families carrying germline deletions of the CDH1 locus. The first 17 bars represent signal obtained with MLPA probes within the CDH1 gene. Please note that for exon 1, three probes were used (1a, 1b and 1c). CDH1 deletions are represented, in the graph, by smaller bars marked with arrows. Bars on the right hand-side represent results obtained with control probes for MLPA (n = 15).
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DDP046F1: MLPA output from the six HDGC families carrying germline deletions of the CDH1 locus. The first 17 bars represent signal obtained with MLPA probes within the CDH1 gene. Please note that for exon 1, three probes were used (1a, 1b and 1c). CDH1 deletions are represented, in the graph, by smaller bars marked with arrows. Bars on the right hand-side represent results obtained with control probes for MLPA (n = 15).

Mentions: We found that six out of the 93 (6.5%) probands showed abnormal multiplex ligation-dependent probe amplification (MLPA) features when compared with the controls, displaying an ∼70% signal reduction in one or more exons of the CDH1 gene and, suggesting the presence of large deletions affecting the CDH1 locus (Fig. 1, Table 1). No abnormalities were observed in the remaining 87 probands.


Germline CDH1 deletions in hereditary diffuse gastric cancer families.

Oliveira C, Senz J, Kaurah P, Pinheiro H, Sanges R, Haegert A, Corso G, Schouten J, Fitzgerald R, Vogelsang H, Keller G, Dwerryhouse S, Grimmer D, Chin SF, Yang HK, Jackson CE, Seruca R, Roviello F, Stupka E, Caldas C, Huntsman D - Hum. Mol. Genet. (2009)

MLPA output from the six HDGC families carrying germline deletions of the CDH1 locus. The first 17 bars represent signal obtained with MLPA probes within the CDH1 gene. Please note that for exon 1, three probes were used (1a, 1b and 1c). CDH1 deletions are represented, in the graph, by smaller bars marked with arrows. Bars on the right hand-side represent results obtained with control probes for MLPA (n = 15).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2667284&req=5

DDP046F1: MLPA output from the six HDGC families carrying germline deletions of the CDH1 locus. The first 17 bars represent signal obtained with MLPA probes within the CDH1 gene. Please note that for exon 1, three probes were used (1a, 1b and 1c). CDH1 deletions are represented, in the graph, by smaller bars marked with arrows. Bars on the right hand-side represent results obtained with control probes for MLPA (n = 15).
Mentions: We found that six out of the 93 (6.5%) probands showed abnormal multiplex ligation-dependent probe amplification (MLPA) features when compared with the controls, displaying an ∼70% signal reduction in one or more exons of the CDH1 gene and, suggesting the presence of large deletions affecting the CDH1 locus (Fig. 1, Table 1). No abnormalities were observed in the remaining 87 probands.

Bottom Line: The statistically significant over-representation of Alus around breakpoints indicates it as a likely mechanism for these deletions.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Pathology and Immunology, University of Porto, Portugal.

ABSTRACT
Germline CDH1 point or small frameshift mutations can be 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 and 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 germline CDH1 point or small frameshift mutations. We screened germline DNA from the 93 mutation negative probands for large genomic rearrangements by Multiplex Ligation-Dependent Probe Amplification. 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 the 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 (UK and North America), carried genomic deletions (UK and North America). Two families carried an identical deletion spanning 193 593 bp, 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.

Show MeSH
Related in: MedlinePlus