A number of studies have implicated PALB2
gene mutations as a rare, but important, contributing factor to hereditary breast cancer (Tischkowitz and Xia, 2010
). The results presented here support these findings in a population-based setting, and confirm that women with germline PALB2
mutations also have an increased risk of CBC. Although only five clearly pathogenic mutations were identified in the group of 1124 women, all of these occurred among the cases. The penetrance of PALB2
gene mutations was originally estimated to be associated with a 2.3-fold increased risk (Rahman, et al., 2007
) but subsequent studies suggested this could be higher, at least for specific mutations (Erkko, et al., 2008
; Southey, et al., 2010
). The relative risk estimate of 5.3 from our study is indeed higher, although this estimate needs to be interpreted with caution given the small number of carriers and carrier relatives in our study and the correspondingly wide confidence intervals.
Despite a large number of published studies, to date no definitely pathogenic PALB2 missense variants have been identified, suggesting that they are non-existent or rare. Our results are consistent with this literature. As an analogy, in the breast cancer predisposing genes BRCA1 and BRCA2 the vast majority of missense variants are neutral, but a few deleterious variants have been identified. The identification of isolated, individual deleterious mutations using case-control studies requires very large numbers of subjects, or evidence that particular types of missense variants are deleterious collectively, allowing aggregation of the data to create sufficient statistical power. Our hierarchical modeling (data not shown) was designed for this purpose, but did not uncover any trends of this nature. Thus, our study does not rule out the possibility that isolated missense PALB2 mutations may be deleterious, but it offers no strong evidence that this is a likely possibility.
The clinical significance of our observation that rare intronic variants are more frequent in the CBC cohort is unclear as none of these variants were predicted to be pathogenic by affecting splicing and only one has been reported previously. Further investigations to address this would involve studying these variants in additional breast cancer cohorts and, at the cellular level, looking for possible functional effects such as diminished BRCA2
binding capacity and reduced homologous recombination efficiency (Tischkowitz, et al., 2007
). It should also be noted that we did not see an increased incidence of breast cancer in first degree relatives of carriers of rare intronic variants which would argue against these being pathogenic.
Our study was conducted using population-based series of breast cancers and as such it avoids the potential problem of ascertainment bias that can occur in cohorts derived from familial cancer clinics or other high-risk settings. Nevertheless, our study has some limitations. First, while a large number of women were screened for PALB2
mutations, the relative rarity of these mutations meant that only a small number of pathogenic mutations were identified. Second, because the study excluded women with synchronous cancers and women who underwent prophylactic contralateral mastectomy following initial breast cancer, and included only women who survived their initial breast cancer, the results may underestimate the overall mutation prevalence. Lastly, we used High Resolution Melting analysis which, as with conventional sequencing, would miss detection of large exon deletions. However, based on our previous experience on the rarity of PALB2
exon deletions (Tischkowitz, et al., 2009
) it is unlikely that we would have missed a significant number of mutations.
In summary, we have confirmed that germline deleterious truncating PALB2 mutations are associated with breast cancer in a population-based case-control study. Although PALB2 mutations are a rare cause of breast cancer, their overrepresentation in the cohort of women with CBC is relevant to the clinical management of newly diagnosed women with breast cancer who are found to be PALB2 mutation carriers as it implies a significant risk of developing a second breast cancer. Our study also provides suggestive evidence that rare intronic variants may be associated with risk, but this finding requires careful validation.