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Numerous variants of unknown significance (VUSs) exist in hereditary breast and ovarian cancers. Although multiple methods have been developed to assess the significance of BRCA1/2variants, functional discrepancies among these approaches remain. Therefore, a comprehensive functional evaluation system for these variants should be established. We performed conventional homologous recombination (HR) assays for 50 BRCA1and 108 BRCA2VUSs and complementarily predicted VUSs using a statistical logistic regression prediction model that integrated six in silico functional prediction tools. BRCA1/2VUSs were classified according to the results of the integrative in vitro and in silico analyses. Using HR assays, we identified 10 BRCA1and 4 BRCA2VUSs as low-functional pathogenic variants. For in silico prediction, the statistical prediction model showed high accuracy for both BRCA1and BRCA2compared with each in silico prediction tool individually and predicted nine BRCA1and seven BRCA2variants to be pathogenic. Integrative functional evaluation in this study and the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines strongly suggested that seven BRCA1variants (p.Glu272Gly, p.Lys1095Glu, p.Val1653Leu, p.Thr1681Pro, p.Phe1761Val, p.Thr1773Ile, and p.Gly1803Ser) and four BRCA2variants (p.Trp31Gly, p.Ser2616Phe, p.Tyr2660Cys, and p.Leu2792Arg) were pathogenic. This study demonstrates that integrative evaluation using conventional HR assays and optimized in silico prediction comprehensively classified the significance of BRCAVUSs for future clinical applications.

We previously reported that L63X and Q934X are BRCA1common founder variants in Japan. So far, there have been no reports of a correlation between such BRCAcommon variants and the risk of BRCA-related cancers. In this analysis, we investigated the correlation between the risk of ovarian cancer (OC) and BRCArecurrent pathogenic variants. We examined the database of the Japanese organization of hereditary breast and ovarian cancer. The database contained 3517 probands who underwent BRCAgenetic testing. Among them, 11.1% (392/3517) had germline BRCA1pathogenic variant, and 8.3% (293/3517) had BRCA2pathogenic variant. We calculated the OC prevalence, breast cancer (BC) prevalence, and the ratio of OC to BC within second-degree relatives. The ratio of OC to BC in Q934X family members was significantly higher than that in the overall BRCA1family members (0.80 vs.0.52: p= 0.038), and the ratio in STOP799 was 0.42, which was relatively lower than the overall BRCA1value. Both Q934X and STOP799 are located in the ovarian cancer cluster region (OCCR), however there seems to be a difference in the risk of OC. R2318X family members had a significant higher ratio of OC to BC at 0.32 than the overall BRCA2value of 0.13 (p= 0.012). R2318X is known to be located in the OCCR. This is the first report to investigate the correlation between BRCArecurrent variants and the risk of OC in Japan. The family members of probands with Q934X or R2318X have a higher risk of OC than that with other BRCAvariants.

This study aimed to clarify the breast cancer prognosis in Japanese patients with BRCA1/2pathogenic variant. We analyzed 2235 women with breast cancer who underwent BRCA1/2genetic testing between 1996 and 2018 using data from the Japanese hereditary breast and ovarian cancer syndrome registry. The cumulative risk for contralateral and ipsilateral breast cancers and time to death since the first breast cancer were stratified based on the BRCA1/2variant status. The median follow-up was 3.0 years (0.1–34.1 years) after the first breast cancer. The annual average risks of contralateral breast cancer in BRCA1and BRCA2and non-BRCA1/2pathogenic variant carriers were 4.0%, 2.9%, and 1.9%, respectively (P= 0.001). The annual average risks of ipsilateral breast cancer in the three groups were 2.7%, 1.4%, and 1.1%, respectively (P= 0.06). BRCA1pathogenic variant carriers had significantly higher risks of contralateral (hazard ratio 1.91, P< 0.001) and ipsilateral (hazard ratio 2.00, P= 0.02) breast cancers than non-BRCA1/2pathogenic variant carriers. The time to death by the BRCA1/2variant status was not significantly difference (P= 0.28). The prognosis of breast cancer patients who received standard treatment was comparable regardless of the BRCA1/2variant status.

Lynch syndrome (LS) is an autosomal dominantly inherited disease predisposed to not only colorectal cancer but also other LS-related tumors. Although the clinical and genetic characteristics of LS in Western countries have been well characterized, the information of Japanese LS is limited. As a collaborative study of Japanese Society for Cancer of the Colon and Rectum (JSCCR), we registered colorectal cancer (CRC) patients who fulfilled the modified Amsterdam II criteria including gastric cancer as an LS-related tumor. Among 4030 CRC patients initially registered in this project, 85 patients (2.1%) fulfilled the modified criteria. An additional 26 patients who met the same criteria were enrolled in the analysis. We analyzed three major responsible genes, MLH1, MSH2, and MSH6by direct sequencing, and further performed multiplex ligation-dependent probe amplification for MLH1and MSH2. Consequently, we identified pathogenic variants in 64 of the 111 patients comprising of 34 patients in MLH1, 28 in MSH2, and 2 in MSH6. It is of note that large structural alterations were found in 17 patients. Among the 64 patients, 11 patients would not have been enrolled in the analysis if gastric cancer were not included in the modified criteria. In addition, 10 of the 64 variant carriers (15.6%) had medical history of gastric cancer. Furthermore, the standardized incidence ratio of gastric cancer in the LS patients to the Japanese population is estimated to be as high as 20.2. These data underscore the importance of gastric cancer in the diagnosis and healthcare of Japanese LS patients.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.