Caution should be taken in the methodology used to confirm c.156_157insAlu BRCA2 mutation

Abstract

To the Editor We read with great interest the article by Peixoto et al. [1] about the screening of the c.156_157insAlu BRCA2 mutation in Northern Portugal. As we previously reported, [2] this BRCA2 rearrangement first described by Teugels et al. [3] in a Portuguese family living in Belgium, will surely be the explanation for breast and ovarian cancer risk in several families of Portuguese ancestry. Most of these families have been, as reported by Peixoto et al. [1], considered negative by the usual screening methods. We are writing this letter to comment about the methodology that must be used to confirm the splicing effect of the c.156_157insAlu mutation. Peixoto et al. report RT–PCR data in their paper, that corroborates our own data concerning the segregation of c.156_157insAlu BRCA2 mutation and cancer in individuals from positive families, but this should not be taken as the most appropriate methodology for the confirmation of this rearrangement. The primers used for their RT–PCR reactions amplify not only the pathogenic Alu-mediated splicing product, lacking exon 3, but also a physiologic, ubiquitous splicing product, also exon 3-deficient, observed in individuals with sporadic cancers and healthy persons [4–8]. Although both splicing products lack exon 3, only the one associated with c.156_157insAlu mutation includes at least the first part of BRCA2 exon 10 and this distinguishes them [9]. Primers like the ones used by Peixoto et al., located in exons 1 and 6 of BRCA2 cDNA, amplify (as shown in Fig. 1a of their report) three fragments in all samples, both c.156_157insAlu carriers and wild type carriers. As a confirmation step, RT–PCR is expected to amplify only true positive samples, originating from really positive c.156_157insAlu carriers. Although the authors explain the three bands observed, as a rule, for diagnosis, we should avoid relying on subjective observations like band intensity. For reasons of length, we did not include the reference to the ubiquitous exon 3-defficient transcript in our original paper [2] but we did discuss it when, very pertinently, Diez et al. [4] wrote a letter raising doubts about our methodology to confirm c.156_157insAlu as a pathogenic BRCA2 mutation. They were very well aware of previous data showing a physiological BRCA2 transcript lacking exon 3 [5–8]. Their questions allowed us, in a reply [9], to explain that indeed, we had tried several primers for our RT–PCR confirmation step and eventually chose primers 1FcDNA/ 10RcDNA, first described by Nordling et al. [10], because these never amplify the ubiquitous splicing transcript. As in the case of our families, and in the case of the BRCA2 family described by Nordling et al., they only amplify a BRCA2-mutated associated transcript. Our three-step-PCR (patent pending) was optimized and every step decided after several studies. The first two steps described by Peixoto et al., are so similar to our own that we believe that no false positive was reported: from our experience, with a total of 29 c.156_156insAlu families already diagnosed, if the first two steps are positive the third always confirms it. But BRCA1 and BRCA2 molecular diagnosis has implications for individuals and their families at clinical, emotional, legal and ethical levels. No doubt must remain in the methodologies for screening, P. Machado F. Vaz (&) Molecular Biology Department, Instituto Portugues de Oncologia de Lisboa, Francisco Gentil, Lisbon, Portugal e-mail: fvaz@ipolisboa.min-saude.pt