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Yoshida R, Hagio T, Kaneyasu T, Gotoh O, Osako T, Tanaka N, Amino S, Yaguchi N, Nakashima E, Kitagawa D, Ueno T, Ohno S, Nakajima T, Nakamura S, Miki Y, Hirota T, Takahashi S, Matsuura M, Noda T, Mori S. Pathogenicity assessment of variants for breast cancer susceptibility genes based on BRCAness of tumor sample. Cancer Sci 2021; 112:1310-1319. [PMID: 33421217 PMCID: PMC7935793 DOI: 10.1111/cas.14803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/03/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022] Open
Abstract
Genes involved in the homologous recombination repair pathway—as exemplified by BRCA1, BRCA2, PALB2, ATM, and CHEK2—are frequently associated with hereditary breast and ovarian cancer syndrome. Germline mutations in the loci of these genes with loss of heterozygosity or additional somatic truncation at the WT allele lead to the development of breast cancers with characteristic clinicopathological features and prominent genomic features of homologous recombination deficiency, otherwise referred to as “BRCAness.” Although clinical genetic testing for these and other genes has increased the chances of identifying pathogenic variants, there has also been an increase in the prevalence of variants of uncertain significance, which poses a challenge to patient care because of the difficulties associated with making further clinical decisions. To overcome this challenge, we sought to develop a methodology to reclassify the pathogenicity of these unknown variants using statistical modeling of BRCAness. The model was developed with Lasso logistic regression by comparing 116 genomic attributes derived from 37 BRCA1/2 biallelic mutant and 32 homologous recombination‐quiescent breast cancer exomes. The model showed 95.8% and 86.7% accuracies in the training cohort and The Cancer Genome Atlas validation cohort, respectively. Through application of the model for variant reclassification of homologous recombination‐associated hereditary breast and ovarian cancer causal genes and further assessment with clinicopathological features, we finally identified one likely pathogenic and five likely benign variants. As such, the BRCAness model developed from the tumor exome was robust and provided a reasonable basis for variant reclassification.
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Affiliation(s)
- Reiko Yoshida
- Department of Oncotherapeutic Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Department of Clinical Genetic Oncology, Cancer Institute Hospital (CIH), JFCR, Tokyo, Japan
| | - Taichi Hagio
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, JFCR, Tokyo, Japan
| | - Tomoko Kaneyasu
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, JFCR, Tokyo, Japan
| | - Osamu Gotoh
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, JFCR, Tokyo, Japan
| | - Tomo Osako
- Division of Pathology, Cancer Institute, JFCR, Tokyo, Japan
| | - Norio Tanaka
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, JFCR, Tokyo, Japan
| | - Sayuri Amino
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Genomics-based Cancer Medicine, Cancer Precision Medicine Center, JFCR, Tokyo, Japan
| | - Noriko Yaguchi
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, JFCR, Tokyo, Japan
| | | | - Dai Kitagawa
- Breast Oncology Center, CIH, JFCR, Tokyo, Japan.,Department of Breast Surgical Oncology, Center Hospital of the National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Shinji Ohno
- Breast Oncology Center, CIH, JFCR, Tokyo, Japan
| | - Takeshi Nakajima
- Department of Clinical Genetic Oncology, Cancer Institute Hospital (CIH), JFCR, Tokyo, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Showa University School of Medicine, Tokyo, Japan
| | - Yoshio Miki
- Division of Genetic Diagnosis, Cancer Institute, JFCR, Tokyo, Japan
| | - Toru Hirota
- Department of Cellular and Molecular Imaging of Cancer, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Division of Experimental Pathology, Cancer Institute, JFCR, Tokyo, Japan
| | - Shunji Takahashi
- Department of Oncotherapeutic Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Medical Oncology, CIH, JFCR, Tokyo, Japan
| | - Masaaki Matsuura
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Tetsuo Noda
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Genomics-based Cancer Medicine, Cancer Precision Medicine Center, JFCR, Tokyo, Japan.,Cancer, Institute, JFCR, Tokyo, Japan
| | - Seiichi Mori
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan.,Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, JFCR, Tokyo, Japan
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Kaneyasu T, Mori S, Yamauchi H, Ohsumi S, Ohno S, Aoki D, Baba S, Kawano J, Miki Y, Matsumoto N, Nagasaki M, Yoshida R, Akashi-Tanaka S, Iwase T, Kitagawa D, Masuda K, Hirasawa A, Arai M, Takei J, Ide Y, Gotoh O, Yaguchi N, Nishi M, Kaneko K, Matsuyama Y, Okawa M, Suzuki M, Nezu A, Yokoyama S, Amino S, Inuzuka M, Noda T, Nakamura S. Prevalence of disease-causing genes in Japanese patients with BRCA1/2-wildtype hereditary breast and ovarian cancer syndrome. NPJ Breast Cancer 2020; 6:25. [PMID: 32566746 PMCID: PMC7293299 DOI: 10.1038/s41523-020-0163-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/30/2020] [Indexed: 12/30/2022] Open
Abstract
Panel sequencing of susceptibility genes for hereditary breast and ovarian cancer (HBOC) syndrome has uncovered numerous germline variants; however, their pathogenic relevance and ethnic diversity remain unclear. Here, we examined the prevalence of germline variants among 568 Japanese patients with BRCA1/2-wildtype HBOC syndrome and a strong family history. Pathogenic or likely pathogenic variants were identified on 12 causal genes for 37 cases (6.5%), with recurrence for 4 SNVs/indels and 1 CNV. Comparisons with non-cancer east-Asian populations and European familial breast cancer cohorts revealed significant enrichment of PALB2, BARD1, and BLM mutations. Younger onset was associated with but not predictive of these mutations. Significant somatic loss-of-function alterations were confirmed on the wildtype alleles of genes with germline mutations, including PALB2 additional somatic truncations. This study highlights Japanese-associated germline mutations among patients with BRCA1/2 wildtype HBOC syndrome and a strong family history, and provides evidence for the medical care of this high-risk population.
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Affiliation(s)
- Tomoko Kaneyasu
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Seiichi Mori
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Hideko Yamauchi
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Shozo Ohsumi
- National Hospital Organization Shikoku Cancer Center, 160 Kou, Minamiumemoto-machi, Matsuyama, Ehime Japan
| | - Shinji Ohno
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Daisuke Aoki
- Department of Obstetrics & Gynecology, Keio University School of Medicine, 35 Shinano-cho, Shinjuku-ku Tokyo, Japan
| | - Shinichi Baba
- Sagara Hospital, 3-31 Matsubara-cho, Kagoshima, Japan
| | - Junko Kawano
- Sagara Hospital, 3-31 Matsubara-cho, Kagoshima, Japan
| | - Yoshio Miki
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku Yokohama, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi Japan
| | - Reiko Yoshida
- Department of Clinical Genetic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Sadako Akashi-Tanaka
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Takuji Iwase
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Dai Kitagawa
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Kenta Masuda
- Department of Obstetrics & Gynecology, Keio University School of Medicine, 35 Shinano-cho, Shinjuku-ku Tokyo, Japan
| | - Akira Hirasawa
- Department of Obstetrics & Gynecology, Keio University School of Medicine, 35 Shinano-cho, Shinjuku-ku Tokyo, Japan
| | - Masami Arai
- Department of Clinical Genetic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Junko Takei
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Yoshimi Ide
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Osamu Gotoh
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Noriko Yaguchi
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Mitsuyo Nishi
- Sagara Hospital, 3-31 Matsubara-cho, Kagoshima, Japan
| | - Keika Kaneko
- National Hospital Organization Shikoku Cancer Center, 160 Kou, Minamiumemoto-machi, Matsuyama, Ehime Japan
| | - Yumi Matsuyama
- National Hospital Organization Shikoku Cancer Center, 160 Kou, Minamiumemoto-machi, Matsuyama, Ehime Japan
| | - Megumi Okawa
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Misato Suzuki
- Department of Breast Surgical Oncology, St. Luke’s International Hospital, 10-1 Akashi-cho, Chuo-ku Tokyo, Japan
| | - Aya Nezu
- Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Shiro Yokoyama
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Sayuri Amino
- Project for Development of Innovative Research on Cancer Therapeutics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Mayuko Inuzuka
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
| | - Tetsuo Noda
- Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku Tokyo, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku Tokyo, Japan
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