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An entire exon 3 germ-line rearrangement in the BRCA2 gene: pathogenic relevance of exon 3 deletion in breast cancer predisposition.

Muller D, Rouleau E, Schultz I, Caputo S, Lefol C, Bièche I, Caron O, Noguès C, Limacher JM, Demange L, Lidereau R, Fricker JP, Abecassis J - BMC Med. Genet. (2011)

Bottom Line: Deletion of exon 3, which is in phase, does not alter the reading frame.Exclusive expression of the delta3 transcript by the mutant allele and segregation data provide evidence for a causal effect of the exon 3 deletion.In addition, our findings suggest that, to interpret the pathogenic effect of any variants of exon 3, both accurate transcript quantification and co-segregation analysis are required.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of oncogenetic, Department of Biology and Pathology, Regional Cancer Centre Paul Strauss, BP30042, 67065 Strasbourg, France. dmuller@strasbourg.fnclcc.fr

ABSTRACT

Background: Germ-line mutations in the BRCA1 and BRCA2 genes are major contributors to hereditary breast/ovarian cancer. Large rearrangements are less frequent in the BRCA2 gene than in BRCA1. We report, here, the first total deletion of exon 3 in the BRCA2 gene that was detected during screening of 2058 index cases from breast/ovarian cancer families for BRCA2 large rearrangements. Deletion of exon 3, which is in phase, does not alter the reading frame. Low levels of alternative transcripts lacking exon 3 (Δ3 delta3 transcript) have been reported in normal tissues, which raises the question whether deletion of exon 3 is pathogenic.

Methods: Large BRCA2 rearrangements were analysed by QMPSF (Quantitative Multiplex PCR of Short Fluorescent Fragments) or MLPA (Multiplex Ligation-Dependent Probe Amplification). The exon 3 deletion was characterized with a "zoom-in" dedicated CGH array to the BRCA2 gene and sequencing. To determine the effect of exon 3 deletion and assess its pathogenic effect, three methods of transcript quantification were used: fragment analysis of FAM-labelled PCR products, specific allelic expression using an intron 2 polymorphism and competitive quantitative RT-PCR.

Results: Large rearrangements of BRCA2 were detected in six index cases out of 2058 tested (3% of all deleterious BRCA2 mutations). This study reports the first large rearrangement of the BRCA2 gene that includes all of exon 3 and leads to an in frame deletion of exon 3 at the transcriptional level. Thirty five variants in exon 3 and junction regions of BRCA2 are also reported, that contribute to the interpretation of the pathogenicity of the deletion. The quantitative approaches showed that there are three classes of delta3 BRCA2 transcripts (low, moderate and exclusive). Exclusive expression of the delta3 transcript by the mutant allele and segregation data provide evidence for a causal effect of the exon 3 deletion.

Conclusion: This paper highlights that large rearrangements and total deletion of exon 3 in the BRCA2 gene could contribute to hereditary breast and/or ovarian cancer. In addition, our findings suggest that, to interpret the pathogenic effect of any variants of exon 3, both accurate transcript quantification and co-segregation analysis are required.

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Family pedigree (A-2005) of the patient carrying the BRCA2 Δ3 large rearrangement. Pedigree symbols: black figures: affected individuals, diagonal slash: deceased individuals; arrow: proband, E: tested for Δ3 large rearrangement, E+: mutation carrier, E-: non carrier, LNH: Non-Hodgkin lymphoma, ca.: cancer.
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Figure 3: Family pedigree (A-2005) of the patient carrying the BRCA2 Δ3 large rearrangement. Pedigree symbols: black figures: affected individuals, diagonal slash: deceased individuals; arrow: proband, E: tested for Δ3 large rearrangement, E+: mutation carrier, E-: non carrier, LNH: Non-Hodgkin lymphoma, ca.: cancer.

Mentions: Family A-2005 (Figure 3) had a breast cancer family history with 6 assessed breast cancer cases. Four of them, of which the proband (III-2), could be tested and were carriers. The affected mother of the proband could be considered as an obligate carrier. Added to a non affected female cousin (32 years old) who tested positive, the carrier genotype could be established or deduced in six females. Out of them, 5 had developed breast cancer at age 37, 41, 47, 48 and 50 (mean age: 44.6), with bilateral breast cancer in one case (II-5). One female carrier underwent bilateral prophylactic mastectomy at age 32. Penetrance could be estimated at 50% by age 45 and at 100% by age 50. Histopathological data, when available, showed grade II or III, oestrogen-receptor (ER) positive and HER2-negative breast tumours, a phenotype consistent with BRCA2-associated breast cancers. Thus, in this family, the Δ3-LR allele segregated well with affected family members, which is consistent with the hypothesis that Δ3-LR is a deleterious allele.


An entire exon 3 germ-line rearrangement in the BRCA2 gene: pathogenic relevance of exon 3 deletion in breast cancer predisposition.

Muller D, Rouleau E, Schultz I, Caputo S, Lefol C, Bièche I, Caron O, Noguès C, Limacher JM, Demange L, Lidereau R, Fricker JP, Abecassis J - BMC Med. Genet. (2011)

Family pedigree (A-2005) of the patient carrying the BRCA2 Δ3 large rearrangement. Pedigree symbols: black figures: affected individuals, diagonal slash: deceased individuals; arrow: proband, E: tested for Δ3 large rearrangement, E+: mutation carrier, E-: non carrier, LNH: Non-Hodgkin lymphoma, ca.: cancer.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3198910&req=5

Figure 3: Family pedigree (A-2005) of the patient carrying the BRCA2 Δ3 large rearrangement. Pedigree symbols: black figures: affected individuals, diagonal slash: deceased individuals; arrow: proband, E: tested for Δ3 large rearrangement, E+: mutation carrier, E-: non carrier, LNH: Non-Hodgkin lymphoma, ca.: cancer.
Mentions: Family A-2005 (Figure 3) had a breast cancer family history with 6 assessed breast cancer cases. Four of them, of which the proband (III-2), could be tested and were carriers. The affected mother of the proband could be considered as an obligate carrier. Added to a non affected female cousin (32 years old) who tested positive, the carrier genotype could be established or deduced in six females. Out of them, 5 had developed breast cancer at age 37, 41, 47, 48 and 50 (mean age: 44.6), with bilateral breast cancer in one case (II-5). One female carrier underwent bilateral prophylactic mastectomy at age 32. Penetrance could be estimated at 50% by age 45 and at 100% by age 50. Histopathological data, when available, showed grade II or III, oestrogen-receptor (ER) positive and HER2-negative breast tumours, a phenotype consistent with BRCA2-associated breast cancers. Thus, in this family, the Δ3-LR allele segregated well with affected family members, which is consistent with the hypothesis that Δ3-LR is a deleterious allele.

Bottom Line: Deletion of exon 3, which is in phase, does not alter the reading frame.Exclusive expression of the delta3 transcript by the mutant allele and segregation data provide evidence for a causal effect of the exon 3 deletion.In addition, our findings suggest that, to interpret the pathogenic effect of any variants of exon 3, both accurate transcript quantification and co-segregation analysis are required.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of oncogenetic, Department of Biology and Pathology, Regional Cancer Centre Paul Strauss, BP30042, 67065 Strasbourg, France. dmuller@strasbourg.fnclcc.fr

ABSTRACT

Background: Germ-line mutations in the BRCA1 and BRCA2 genes are major contributors to hereditary breast/ovarian cancer. Large rearrangements are less frequent in the BRCA2 gene than in BRCA1. We report, here, the first total deletion of exon 3 in the BRCA2 gene that was detected during screening of 2058 index cases from breast/ovarian cancer families for BRCA2 large rearrangements. Deletion of exon 3, which is in phase, does not alter the reading frame. Low levels of alternative transcripts lacking exon 3 (Δ3 delta3 transcript) have been reported in normal tissues, which raises the question whether deletion of exon 3 is pathogenic.

Methods: Large BRCA2 rearrangements were analysed by QMPSF (Quantitative Multiplex PCR of Short Fluorescent Fragments) or MLPA (Multiplex Ligation-Dependent Probe Amplification). The exon 3 deletion was characterized with a "zoom-in" dedicated CGH array to the BRCA2 gene and sequencing. To determine the effect of exon 3 deletion and assess its pathogenic effect, three methods of transcript quantification were used: fragment analysis of FAM-labelled PCR products, specific allelic expression using an intron 2 polymorphism and competitive quantitative RT-PCR.

Results: Large rearrangements of BRCA2 were detected in six index cases out of 2058 tested (3% of all deleterious BRCA2 mutations). This study reports the first large rearrangement of the BRCA2 gene that includes all of exon 3 and leads to an in frame deletion of exon 3 at the transcriptional level. Thirty five variants in exon 3 and junction regions of BRCA2 are also reported, that contribute to the interpretation of the pathogenicity of the deletion. The quantitative approaches showed that there are three classes of delta3 BRCA2 transcripts (low, moderate and exclusive). Exclusive expression of the delta3 transcript by the mutant allele and segregation data provide evidence for a causal effect of the exon 3 deletion.

Conclusion: This paper highlights that large rearrangements and total deletion of exon 3 in the BRCA2 gene could contribute to hereditary breast and/or ovarian cancer. In addition, our findings suggest that, to interpret the pathogenic effect of any variants of exon 3, both accurate transcript quantification and co-segregation analysis are required.

Show MeSH
Related in: MedlinePlus