This Article Full Text (PDF) Purchase Article View Shopping Cart Alert me when this article is cited Alert me if a correction is posted Services Email this article to a colleague Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Save to my personal folders Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Capalbo, C. Articles by Giannini, G. Search for Related Content PubMed PubMed Citation Articles by Capalbo, C. Articles by Giannini, G.

Does the Search for Large Genomic Rearrangements Impact BRCAPRO Carrier Prediction?

Department of Experimental Medicine and Pathology, University La Sapienza, Rome, Italy

Enrico Ricevuto

Department of Experimental Medicine, University of L'Aquila, L'Aquila, Italy

Christian Rinaldi

Neuromed Institute, Pozzilli, Italy

Massimo Zani, Sergio Ferraro

Department of Experimental Medicine and Pathology, University La Sapienza, Rome, Italy

Luigi Frati

Department of Experimental Medicine and Pathology, University La Sapienza, Rome; and the Neuromed Institute, Pozzilli, Italy

Isabella Screpanti

Department of Experimental Medicine and Pathology, University La Sapienza, Rome, Italy

Alberto Gulino

Department of Experimental Medicine and Pathology, University La Sapienza, Rome; and the Neuromed Institute, Pozzilli, Italy

Giuseppe Giannini

Department of Experimental Medicine and Pathology, University La Sapienza, Rome, Italy

To the Editor:

Recently, several models have been developed to help in the selection of individuals with the high probability of being BRCA1/2 mutation carriers^1-5 and an expanding debate is trying to assess whether any of them might be considered sufficiently validated. Although some criticisms are also present,⁶ many authors agree that BRCAPRO and BOADICEA (among the genetic models) and Myriad II (among the empirical models) show similar performances and might be useful tools in identifying possible BRCA1/2 mutations carriers.^7,8 The Italian Consortium for Hereditary Breast and Ovarian Cancer proposed a country-customized version of the BRCAPRO software (IC software) that increased BRCAPRO performances in the Italian population.⁹ We contributed to the topic by validating the IC software in an independent data set.¹⁰

A common observation among BRCAPRO users is that prediction accuracy improves as the threshold probability increases. In particular, we believe that an IC software carrier indeed identifies 80% of probands with genetic mutations responsible for the inherited breast/ovarian cancer syndrome observed in a family, independent of their genetic test results. The apparent failures in such predictions are most likely dependent on the level of laboratory methods used for genetic analysis. Agreement on this speculation also comes from the recent article by James et al.¹¹ In assessing the performances of different models, they also postulated, but not demonstrated, that the apparent failures of their most accurate model (BRCAPRO) in predicting high carrier probability risk (> 90%) in 5% of the BRCA mutation-negative families might be at least partially explained by the occurrence of large genomic rearrangements in BRCA genes. Our recent data provide evidence supporting this hypothesis.

Indeed, we have screened our series, previously tested for deleterious point mutations, searching for BRCA1 and BRCA2 genomic rearrangements. In brief, for each family we selected a breast and/or ovarian cancer-affected individual as the index case (proband). The entire coding sequences and each intron/exon boundary of BRCA1 and BRCA2 were screened by protein truncation test (limited to BRCA1 exon 11) and/or direct sequencing. The 83 probands with no detectable BRCA1/2 point mutations were further screened by multiple ligation probe amplification (MLPA). For each proband, the a priori probability of carrying a pathogenic BRCA1/2 germline mutation was calculated by the IC software version 3.4, the Italian country-customized version of BRCAPRO. Index cases were classified as carrier positive or carrier negative with a threshold of 10% mutation carrier probability.

Of 112 probands selected according to specific criteria previously reported,¹² 29 patients had BRCA1/2 point mutations (Table 1) and two showed BRCA1 rearrangements (deletion of exons 23 and 24 and exons 18 and 19, for patient BR59 and BR95, respectively).¹³ No BRCA2 rearrangements were detected. The IC software identified 75 carrier-positive probands and pathogenic BRCA1/2 mutations were detected in 25 of them, performing a high sensitivity (86%) and negative predictive value (89%). As mentioned, prediction accuracy improved as the threshold probability increased and in particular in the high-risk group (defined as mutation carrier probability 80%) we counted approximately 50% of the total 29 BRCA1/2 point mutations. Interestingly 72.2% of the probands assigned to this subgroup were point mutation positive, only five being point mutation negative. In contrast, in the moderate-risk group (defined as mutation carrier probability 10% and < 80%) only 12 of 57 (21%) probands were in fact point mutations positive. This difference was statistically significant (P < .0001, Table 1), indicating that the IC software 80% carrier probability prediction is strongly suggestive for the presence of a pathogenic genetic alteration. To test whether other genetic alterations were present in the BRCA1/2 point mutations negative probands with IC carrier probability 80%, we searched our series for BRCA1/2 large genomic rearrangements. Indeed by MLPA analysis, we showed that two of five probands belonging to this subgroup showed BRCA1 rearrangements. This further raised the mutation frequency in the IC carrier probability 80% group from 72.2% to 83.3%, while it did not change for the moderate-risk group (Table 2). Only three probands belonging to the high-risk group remained mutation negative. However, we cannot rule out the possibility that genetic alterations in other site of the BRCA1/2 genes (such as the promoter region) or even in other breast cancer related genes could be found in these subjects. This is also in agreement with the level of sensitivity of the current methodologies which, even in the most accurate hands, does not seem to exceed 85% to 95%.¹⁴

In conclusion, we provide evidence that breast/ovarian cancer families with IC software carrier probability prediction 80% indeed have mutations on the BRCA genes in more than 80% of patients and that large genomic rearrangements were found in more than 10% of these probands. Based on these data and pushing forward the original hypothesis, we believe that probably all the probands with a carrier probability prediction 80% determined by the BRCAPRO (and its Italian country-customized version) have to be considered as carriers of a strongly predisposing genetic alteration either in the BRCA1/2 genes or in other yet undescribed gene locations, independent of our ability to detect such mutations.

AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST

The author(s) indicated no potential conflicts of interest.

ACKNOWLEDGMENTS

Supported by grants from Associazione Italiana per la Ricerca sul Cancro, Ministry of Health, the National Research Council (CNR), the Ministry of University and Research, the Pasteur Institute, and the Cenci-Bolognetti Foundation.

REFERENCES

1. Berry DA, Iversen ES Jr, Gudbjartsson DF, et al: BRCAPRO validation, sensitivity of genetic testing of BRCA1/BRCA2, and prevalence of other breast cancer susceptibility genes. J Clin Oncol 20:2701-2712, 2002[Abstract/Free Full Text]

2. Evans DG, Eccles DM, Rahman N, et al: A new scoring system for the chances of identifying a BRCA1/2 mutation outperforms existing models including BRCAPRO. J Med Genet 41:474-480, 2004[Abstract/Free Full Text]

3. Frank TS, Deffenbaugh AM, Reid JE, et al: Clinical characteristics of individuals with germline mutations in BRCA1 and BRCA2: Analysis of 10,000 individuals. J Clin Oncol 20:1480-1490, 2002[Abstract/Free Full Text]

4. Antoniou AC, Pharoah PP, Smith P, et al: The BOADICEA model of genetic susceptibility to breast and ovarian cancer. Br J Cancer 91:1580-1590, 2004[Medline]

5. Antoniou AC, Easton DF: Risk prediction models for familial breast cancer. Future Oncol 2:257-274, 2006[CrossRef][Medline]

6. Kang HH, Williams R, Leary J, et al: Evaluation of models to predict BRCA germline mutations. Br J Cancer 95:914-920, 2006[CrossRef][Medline]

7. Barcenas CH, Hosain GM, Arun B, et al: Assessing BRCA carrier probabilities in extended families. J Clin Oncol 24:354-360, 2006[Abstract/Free Full Text]

8. Antoniou AC, Durocher F, Smith P, et al: BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families. Breast Cancer Res 8:R3, 2006[CrossRef][Medline]

9. Marroni F, Aretini P, D'Andrea E, et al: Evaluation of widely used models for predicting BRCA1 and BRCA2 mutations. J Med Genet 41:278-285, 2004[Free Full Text]

10. Capalbo C, Ricevuto E, Vestri A, et al: Improving the accuracy of BRCA1/2 mutation prediction: Validation of the novel country-customized IC software. Eur J Hum Genet 14:49-54, 2006[Medline]

11. James PA, Doherty R, Harris M, et al: Optimal selection of individuals for BRCA mutation testing: A comparison of available methods. J Clin Oncol 24:707-715, 2006[Abstract/Free Full Text]

12. Giannini G, Capalbo C, Ristori E, et al: Novel BRCA1 and BRCA2 germline mutations and assessment of mutation spectrum and prevalence in Italian breast and/or ovarian cancer families. Breast Cancer Res Treat 100:83-91, 2006[CrossRef][Medline]

13. Buffone A, Capalbo C, Ricevulo E, et al: Prevalence of BRCA1 and BRCA2 genomic rearrangements in a cohort of consecutive Italian breast and/or ovarian cancer families. Breast Cancer Res Treat [Epub ahead of print February 28, 2007]

14. Evans DG, Bulman M, Young K, et al: Sensitivity of BRCA1/2 mutation testing in 466 breast/ovarian cancer families. J Med Genet 40:e107, 2003[Free Full Text]

15. Capalbo C, Ricevuto E, Vestri A, et al: BRCA1 and BRCA2 genetic testing in Italian breast and/or ovarian cancer families: Mutation spectrum and prevalence and analysis of mutation prediction models. Ann Oncol 17:vii34-vii40, 2006 (suppl 7)[Abstract/Free Full Text]

This article has been cited by other articles:

				G. Giannini, C. Capalbo, L. Ottini, A. Buffone, L. De Marchis, E. Margaria, D. Vitolo, E. Ricevuto, C. Rinaldi, M. Zani, et al. Clinical Classification of BRCA1 DNA Missense Variants: H1686Q Is a Novel Pathogenic Mutation Occurring in the Ontogenetically Invariant THV Motif of the N-Terminal BRCT Domain J. Clin. Oncol., September 1, 2008; 26(25): 4212 - 4214. [Full Text] [PDF]

This Article Full Text (PDF) Purchase Article View Shopping Cart Alert me when this article is cited Alert me if a correction is posted Services Email this article to a colleague Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Save to my personal folders Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Capalbo, C. Articles by Giannini, G. Search for Related Content PubMed PubMed Citation Articles by Capalbo, C. Articles by Giannini, G.