Differentiating pathogenic mutations from polymorphic alterations in the splice sites of <i>BRCA1</i> and <i>BRCA2</i>

Claes, Kathleen; Poppe, Bruce; Coene, Ilse; Foretová, Lenka; Paepe, Anne De; Messiaen, Ludwine

doi:10.1002/gcc.10221

Cited by 81 publications

(76 citation statements)

References 22 publications

(20 reference statements)

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“…Four K3326X variant carriers also harbored the IVS 24-16T>C polymorphism, previously described as associated with K3326X. This intronic polymorphism is not thought to be deleterious (Claes et al, 2003). One of these four patients also had an IVS 16-2A>G mutation, which is suspected to be deleterious.…”

Section: Resultsmentioning

confidence: 74%

“…Subsequently Krainer et al (1997) described this mutation in a single case in a cohort of 73 early-onset breast cancers and did not find it in an age-and sex-matched control group of 130 individuals. The K3326X polymorphism has since been identified in patients with a variety of cancers either alone or in combination with obvious pathogenic mutations (Haraldsson et al, 1998;Claes et al, 2003). Recently, evidence that the K3326X polymorphism may be functionally deleterious came from Howlett and coworkers who, in demonstrating that biallelic inactivation of BRCA2 was a cause of Fanconi's anemia identified a Fanconi anemia individual with the K3326X variant as well as the 3033delAAAC frameshift mutation on exon 11, suggesting that the variant may cause Fanconi's anemia in the compound heterozygote state (Howlett et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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Increased prevalence of the BRCA2 polymorphic stop codon K3326X among individuals with familial pancreatic cancer

et al. 2005

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Germline BRCA2 mutations predispose to the development of pancreatic cancer. A polymorphic stop codon in the coding region of BRCA2 (K3326X) has been described, and although an initial epidemiological study suggested it was not disease causing, subsequent studies have been inconclusive. To investigate the biological significance of the K3326X polymorphism, we determined its prevalence in patients with sporadic and familial pancreatic cancer. Using a case-control design, we studied 250 patients with resected sporadic pancreatic adenocarcinomas, 144 patients with familial pancreatic adenocarcinoma, 115 spouses of patients with pancreatic cancer, and a disease control group of 135 patients without a personal history of cancer who had undergone cholecystectomy for non-neoplastic disease. The K3326X polymorphism was detected using heteroduplex analysis and DNA sequencing. The BRCA2 K3326X polymorphism was significantly more prevalent in individuals with familial pancreatic cancer: 8/144 (5.6%) vs 3/250 controls (1.2%) (odds ratio, 4.84; 95% CI, 1.27-18.55, Po0.01). One K3326X carrier with familial pancreatic cancer carried an alteration (IVS 16-2A>G) suspected to be deleterious. Excluding this case did not alter the significance of the association (OR: 4.24, Po0.01). In contrast, there was no difference in prevalence among individuals with sporadic pancreatic cancer -7/250 (OR: 2.37, 95% CI: 0.61-9.27). The increased prevalence of the BRCA2 K3326X polymorphism in patients with familial pancreatic cancer suggests that this polymorphism is deleterious and contributes to pancreatic cancer risk.

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Section: Resultsmentioning

confidence: 74%

Section: Introductionmentioning

confidence: 99%

Increased prevalence of the BRCA2 polymorphic stop codon K3326X among individuals with familial pancreatic cancer

et al. 2005

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“…For BRCA2, an 'Ovarian Cancer Cluster Region' (OCCR) in the middle third of the gene was proposed by Gayther et al (1997). Surprisingly, in our study no ovarian cancer cases were recorded Figure 2 RT -PCR was performed with primers spanning exons 11 -15 of the BRCA2 gene (nucleotides 6948 -7714; GenBank accession number NM_000059) on RNA extracted from lymphocytes as described by Claes et al (2003). RT -PCR on RNA from the patient carrying BRCA2 R2336H (lane 1) showed a full-length fragment of 767 bp and three faster migrating bands (697 bp: skipping of out of frame exon 13 (stop 2345); 671 bp: skipping of in-frame exon 12 (deletion of 32 amino acids); 601 bp: skipping of out of frame exons 12 and 13 (stop 2311)).…”

Section: Variation In Cancer Risk By Mutation Positionmentioning

confidence: 84%

“…Y42 is a highly conserved amino acid and Y to C is a radical amino-acid change, compromising in vivo the interaction between BRCA2 and replication protein A (Wong et al, 2003). All splice site mutations were studied at the RNA level Claes et al, 2003). RT -PCR analysis for BRCA2 R2336H in the last codon of exon 13 was not yet described and revealed the wild-type allele and three smaller transcripts, representing a complete loss of exon 13, loss of exon 12 and loss of exons 12 and 13.…”

Section: Brca1 and Brca2 Mutationsmentioning

confidence: 99%

BRCA1 and BRCA2 germline mutation spectrum and frequencies in Belgian breast/ovarian cancer families

et al. 2004

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Worldwide variation in the distribution of BRCA1 and BRCA2 mutations is well recognised, and for the Belgian population no comprehensive studies about BRCA1/2 mutation spectra or frequencies have been published. We screened the complete coding region of both genes in 451 individuals from 349 Belgian families referred to a family cancer clinic and identified 49 families with a BRCA1 and 26 families with a BRCA2 mutation. Six major recurrent mutations (BRCA1 IVS5 þ 3A4G, 2478 -2479insG, E1221X and BRCA2 IVS6 þ 1G4A, 6503-6504delTT, 9132delC) accounted for nearly 60% of all mutations identified. Besides 75 true pathogenic mutations, we identified several variants of unknown clinical significance. In combination with a family history, an early average age of female breast cancer diagnosis (Po0.001), and the presence of a relative with ovarian cancer (Po0.0001) or multiple primary breast cancers (P ¼ 0.002), increased the chance for finding a mutation. Male breast cancer was indicative of a BRCA2 mutation segregating in the family (P ¼ 0.002). Mutations in the 5 0 -end of BRCA1 and BRCA2 were associated with a significantly increased risk for ovarian cancer relative to the central portion of the gene. Our study suggests a role for additional breast cancer susceptibility genes in the Belgian population, since mutation detection ratios were low in high-risk breast cancer-only families as compared to breast -ovarian cancer families. Given the large proportion of recurring mutations, molecular testing can now be organised in a more cost-effective way. Our data allow optimisation of genetic counselling and disease prevention in Belgian breast/ovarian cancer families. Since the mapping and the cloning of two genes that confer susceptibility to both breast and ovarian cancer, BRCA1 and BRCA2 (Miki et al, 1994;Wooster et al, 1995;Tavtigian et al, 1996), it became possible to offer genetic testing to families with a predisposition for breast and/or ovarian cancer. Consequently, individuals at risk can now be identified as candidates for surveillance programmes. A large number of distinct mutations in the BRCA1 and BRCA2 genes have been reported worldwide, but population-specific variation in the distribution of BRCA1/2 mutations is well recognised. In some populations or ethnic groups, founder mutations form a sufficient proportion of the total to justify the adoption of specific molecular screening strategies.To date, no comprehensive studies in the Belgian population have been published. Only data from small series are available (Claes et al, 1999a, b) or from studies in which the analysis was restricted to a few BRCA1/2 exons or to BRCA1 only Sibille-Hoang et al, 1998;Goelen et al, 1999). We performed mutation screening of the complete coding region of BRCA1 and BRCA2 in 349 unrelated Belgian families referred to our family cancer clinic and report here the nature and distribution of the mutations identified. We found phenotypic differences between families in whom a disease-causing mutation was identified vs BRCA1/2 muta...

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“…Exon skipping or the activation of a cryptic splice-site leading to deletion of exon sequences or retention of intronic sequences provide strong evidence that the variant is pathogenic. Alternatively, normal mRNA processing indicates that the variants can be considered as neutral variations [Petrij-Bosch et al, 1997;Scholl et al, 1999;Fetzer et al, 1999;Pyne et al, 2000;Laskie et al, 2001;Hofmann et al, 2003;Claes et al, 2003;Campos et al, 2003;Keaton et al, 2003;Brose et al, 2004;Tesoriero et al, 2005;Chen et al, 2006;Bonatti et al, 2006]. Based on the highly conserved sequences, splice-site prediction programs (SSPPs) have been developed to predict the possible effect of a variant on RNA splicing.…”

Section: Introductionmentioning

confidence: 99%

Intronic variants inBRCA1andBRCA2that affect RNA splicing can be reliably selected by splice-site prediction programs

et al. 2009

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A large number of sequence variants identified in BRCA1 and BRCA2 cannot be distinguished as either disease-causing mutations or neutral variants. These so-called unclassified variants (UVs) include variants that are located in the intronic sequences of BRCA1 and BRCA2. The purpose of this study was to assess the use of splice-site prediction programs (SSPPs) to select intronic variants in BRCA1 and BRCA2 that are likely to affect RNA splicing. We performed in vitro molecular characterization of RNA of six intronic variants in BRCA1 and BRCA2. In four cases (BRCA1, c.81-6T4A and c.498615G4T; BRCA2, c.76171 2T4G and c.875415G4A) a deleterious effect on RNA splicing was seen, whereas the c.135-15_-12del variant in BRCA1 showed no effect on RNA splicing. In the case of the BRCA2 c.68-7T4A variant, RNA analysis was not sufficient to establish the clinical significance. Six SSPPs were used to predict whether an effect on RNA splicing was expected for these six variants as well as for 23 intronic variants in BRCA1 for which the effect on RNA splicing has been published. Out of a total of 174 predictions, 161 (93%) were informative (i.e., the wild-type splice-site was recognized). No falsenegative predictions were observed; an effect on RNA splicing was always predicted by these programs. In four cases (2.5%) a false-positive prediction was observed. For DNA diagnostic laboratories, these programs are therefore very useful to select intronic variants that are likely to affect RNA splicing for further analysis.

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Differentiating pathogenic mutations from polymorphic alterations in the splice sites of BRCA1 and BRCA2

Cited by 81 publications

References 22 publications

Increased prevalence of the BRCA2 polymorphic stop codon K3326X among individuals with familial pancreatic cancer

Increased prevalence of the BRCA2 polymorphic stop codon K3326X among individuals with familial pancreatic cancer

BRCA1 and BRCA2 germline mutation spectrum and frequencies in Belgian breast/ovarian cancer families

Intronic variants inBRCA1andBRCA2that affect RNA splicing can be reliably selected by splice-site prediction programs

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