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Hidden SVA retrotransposon insertion in BRCA1 revealed by nanopore targeted sequencing causes hereditary breast and ovarian cancer

Journal of Human Genetics volume 70, pages 503–508 (2025)Cite this article

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Abstract

In Japan, germline BRCA1/2 genetic testing is extensively used for the diagnosis of hereditary breast and ovarian cancer syndrome (HBOC). However, inconclusive results sometimes complicate clinical management. In this study, we identified an intronic SINE-VNTR-Alu (SVA) insertion in BRCA1 of a proband and her mother, both of whom had inconclusive conventional BRCA1/2 genetic test results, by targeted long-read sequencing (LRS) through the application of nanopore adaptive sampling and Flongle genome amplicon sequencing. We further confirmed splicing aberrations using cDNA quantitative PCR with TaqMan probes and Flongle cDNA amplicon sequencing. Our findings highlighted that, in addition to conventional BRCA1/2 genetic testing, structural variation analysis using targeted LRS is indispensable for the accurate diagnosis of HBOC in certain cases. Furthermore, Flongle amplicon sequencing was demonstrated to be effective for sequencing regions refractory to conventional PCR and Sanger sequencing, particularly repetitive and GC-rich regions, such as retrotransposons.

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References

  1. Ueki A, Yoshida R, Kosaka T, Matsubayashi H. Clinical risk management of breast, ovarian, pancreatic, and prostatic cancers for BRCA1/2 variant carriers in Japan. J Hum Genet. 2023;68:517–26.

    Article  PubMed  CAS  Google Scholar 

  2. Maheu C, Vodermaier A, Rothenmund H, Gallinger S, Ardiles P, Semotiuk K, et al. Pancreatic cancer risk counselling and screening: impact on perceived risk and psychological functioning. Fam Cancer. 2010;9:617–24.

    Article  PubMed  Google Scholar 

  3. Hendrickson BC, Judkins T, Ward BD, Eliason K, Deffenbaugh AE, Burbidge LA, et al. Prevalence of five previously reported and recurrent BRCA1 genetic rearrangement mutations in 20,000 patients from hereditary breast/ovarian cancer families. Genes Chromosomes Cancer. 2005;43:309–13.

    Article  PubMed  CAS  Google Scholar 

  4. Nakamura W, Hirata M, Oda S, Chiba K, Okada A, Mateos RN, et al. Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes. NPJ Genom Med. 2024;9:11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Yano N, Chong PF, Kojima KK, Miyoshi T, Luqman-Fatah A, Kimura Y, et al. Long-read sequencing identifies an SVA_D retrotransposon insertion deep within the intron of ATP7A as a novel cause of occipital horn syndrome. J Med Genet. 2024;61:950–8.

    Article  PubMed  CAS  Google Scholar 

  6. Kawakami R, Hiraide T, Watanabe K, Miyamoto S, Hira K, Komatsu K, et al. RNA sequencing and target long-read sequencing reveal an intronic transposon insertion causing aberrant splicing. J Hum Genet. 2024;69:91–9.

    Article  PubMed  CAS  Google Scholar 

  7. Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, et al. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet. 2021;108:1436–49.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Akamatsu S, Mitsuhashi S, Soga K, Mizukami H, Shiraishi M, Frith MC, et al. Targeted nanopore sequencing using the Flongle device to identify mitochondrial DNA variants. Sci Rep. 2024;14:25161.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol. 2006;7:3.

    Article  PubMed  PubMed Central  Google Scholar 

  10. Aneichyk T, Hendriks WT, Yadav R, Shin D, Gao D, Vaine CA, et al. Dissecting the causal mechanism of X-linked Dystonia-Parkinsonism by integrating genome and transcriptome assembly. Cell. 2018;172:897–909.e21.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Dias Nunes J, Demeestere I, Devos M. BRCA mutations and fertility preservation. Int J Mol Sci. 2023;25:204.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Chenais B. Transposable elements in cancer and other human diseases. Curr Cancer Drug Targets. 2015;15:227–42.

    Article  PubMed  CAS  Google Scholar 

  13. Arribas YA, Baudon B, Rotival M, Suárez G, Bonté P-E, Casas V, et al. Transposable element exonization generates a reservoir of evolving and functional protein isoforms. Cell. 2024;187:7603–20.e22.

    Article  PubMed  CAS  Google Scholar 

  14. Ismail T, Alzneika S, Riguene E, Al-Maraghi S, Alabdulrazzak A, Al-Khal N, et al. BRCA1 and its vulnerable C-terminal BRCT domain: structure, function, genetic mutations and links to diagnosis and treatment of breast and ovarian cancer. Pharmaceuticals. 2024;17:333.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Coquelle N, Green R, Glover JNM. Impact of BRCA1 BRCT domain missense substitutions on phosphopeptide recognition. Biochemistry. 2011;50:4579–89.

    Article  PubMed  CAS  Google Scholar 

  16. Lee MS, Green R, Marsillac SM, Coquelle N, Williams RS, Yeung T, et al. Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Cancer Res. 2010;70:4880–90.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Attig J, Ruiz de Los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, et al. Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. Elife. 2016;5:e19545.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Sela N, Kim E, Ast G. The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol. 2010;11:R59.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Petrozziello T, Dios AM, Mueller KA, Vaine CA, Hendriks WT, Glajch KE, et al. SVA insertion in X-linked Dystonia Parkinsonism alters histone H3 acetylation associated with TAF1 gene. PLoS ONE. 2020;15:e0243655.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Bozsik A, Pócza T, Papp J, Vaszkó T, Butz H, Patócs A, et al. Complex characterization of germline large genomic rearrangements of the BRCA1 and BRCA2 genes in high-risk breast cancer patients-novel variants from a large national center. Int J Mol Sci. 2020;21:4650.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Ewald IP, Ribeiro PLI, Palmero EI, Cossio SL, Giugliani R, Ashton-Prolla P. Genomic rearrangements in BRCA1 and BRCA2: a literature review. Genet Mol Biol. 2009;32:437–46.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Yukishige S, Inoue H, Inui T, Sasa S, Misaki M, Goto M, et al. Three cases of inconclusive as results of BRCA genetic testing. J Hered Tumors. 2024;24:147–52. (in Japanese).

    Google Scholar 

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Acknowledgements

We thank the proband and her family for participating in this study. We also thank Tomoko Kozaki at Kitasato University, Eri Nonoyama and Miki Uchiyama at St. Marianna University School of Medicine, and LSI Medience Corporation for technical assistance. This work was supported by grants from the Practical Research Project for Rare/Intractable Diseases of the Japan Agency for Medical Research and Development (AMED, No. ek0109617) (YY) and Japan Society for the Promotion of Science (JSPS) KAKENHI under grant numbers JP24K18897 (SO). Finally, we thank Edanz (https://jp.edanz.com/ac) for editing a draft of this manuscript.

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Authors and Affiliations

  1. Department of Laboratory Medicine, St. Marianna University School of Medicine, Kawasaki, Japan

    Sachiko Ohori & Ohsuke Migita

  2. Department of Clinical Genetics, Kitasato University Hospital, Sagamihara, Japan

    Sachiko Ohori, Mina Waraya, Takafumi Sangai, Naomi Araki, Rika Kawata, Keiko Takahashi & Fumio Takada

  3. Department of Breast and Thyroid Surgery, Kitasato University School of Medicine, Sagamihara, Japan

    Mina Waraya, Kaoru Fujisaki & Takafumi Sangai

  4. Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan

    Satomi Mitsuhashi & Yoshihisa Yamano

  5. Department of Rare Disease Research, St. Marianna University School of Medicine, Kawasaki, Japan

    Yoshihisa Yamano

  6. Department of Medical Genetics and Genomics, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan

    Fumio Takada

Authors
  1. Sachiko Ohori
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  2. Mina Waraya
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  3. Kaoru Fujisaki
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  4. Takafumi Sangai
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  5. Naomi Araki
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  7. Keiko Takahashi
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  8. Ohsuke Migita
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  9. Satomi Mitsuhashi
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  10. Yoshihisa Yamano
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  11. Fumio Takada
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Contributions

SO: conceptualization, formal analysis, investigation, visualization, methodology, funding acquisition, writing—original draft, review, and editing. MW, KF, TS, NA, RK, KT and FT: resources, writing—original draft, review, and editing. OM: methodology, writing—original draft, review, and editing. SM: conceptualization, methodology, writing—original draft, review, and editing. YY: methodology, funding acquisition, writing—original draft, review, and editing.

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Correspondence to Sachiko Ohori or Fumio Takada.

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Ohori, S., Waraya, M., Fujisaki, K. et al. Hidden SVA retrotransposon insertion in BRCA1 revealed by nanopore targeted sequencing causes hereditary breast and ovarian cancer. J Hum Genet 70, 503–508 (2025). https://doi.org/10.1038/s10038-025-01365-7

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