Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Analyses of breakpoint junctions of complex genomic rearrangements comprising multiple consecutive microdeletions by nanopore sequencing


The widespread use of genomic copy number analysis has revealed many previously unknown genomic structural variations, including some which are more complex. In this study, three consecutive microdeletions were identified in the same chromosome by microarray-based comparative genomic hybridization (aCGH) analysis for a patient with a neurodevelopmental disorder. Subsequent fluorescence in situ hybridization (FISH) analyses unexpectedly suggested complicated translocations and inversions. For better understanding of the mechanism, breakpoint junctions were analyzed by nanopore sequencing, as a new long-read whole-genome sequencing (WGS) tool. The results revealed a new chromosomal disruption, giving rise to four junctions in chromosome 7. According the sequencing results of breakpoint junctions, all junctions were considered as the consequence of multiple double-strand breaks and the reassembly of DNA fragments by nonhomologous end-joining, indicating chromothripsis. KMT2E, located within the deletion region, was considered as the gene responsible for the clinical features of the patient. Combinatory usage of aCGH and FISH analyses would be recommended for interpretation of structural variations analyzed through WGS.

Your institute does not have access to this article

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. Sanchis-Juan A, Stephens J, French CE, Gleadall N, Megy K, Penkett C, et al. Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing. Genome Med. 2018;10:95.

    CAS  Article  Google Scholar 

  2. Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, et al. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018;15:461–8.

    CAS  Article  Google Scholar 

  3. Plaisancie J, Kleinfinger P, Cances C, Bazin A, Julia S, Trost D, et al. Constitutional chromoanasynthesis: description of a rare chromosomal event in a patient. Eur J Med Genet. 2014;57:567–70.

    Article  Google Scholar 

  4. Suzuki E, Shima H, Toki M, Hanew K, Matsubara K, Kurahashi H, et al. Complex X-chromosomal rearrangements in two women with ovarian dysfunction: implications of chromothripsis/chromoanasynthesis-dependent and -independent origins of complex genomic alterations. Cytogenet Genome Res. 2016;150:86–92.

    Article  Google Scholar 

  5. Shimojima K, Mano T, Kashiwagi M, Tanabe T, Sugawara M, Okamoto N, et al. Pelizaeus-Merzbacher disease caused by a duplication-inverted triplication-duplication in chromosomal segments including the PLP1 region. Eur J Med Genet. 2012;55:400–3.

    Article  Google Scholar 

  6. Suzuki T, Tsurusaki Y, Nakashima M, Miyake N, Saitsu H, Takeda S, et al. Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing. J Hum Genet. 2014;59:649–54.

    CAS  Article  Google Scholar 

  7. Gong L, Wong CH, Cheng WC, Tjong H, Menghi F, Ngan CY, et al. Picky comprehensively detects high-resolution structural variants in nanopore long reads. Nat Methods. 2018;15:455–60.

    CAS  Article  Google Scholar 

  8. Yamamoto T, Wilsdon A, Joss S, Isidor B, Erlandsson A, Suri M, et al. An emerging phenotype of Xq22 microdeletions in females with severe intellectual disability, hypotonia and behavioral abnormalities. J Hum Genet. 2014;59:300–6.

    CAS  Article  Google Scholar 

  9. Shimojima K, Sugiura C, Takahashi H, Ikegami M, Takahashi Y, Ohno K, et al. Genomic copy number variations at 17p13.3 and epileptogenesis. Epilepsy Res. 2010;89:303–9.

    CAS  Article  Google Scholar 

  10. Shimojima K, Komoike Y, Tohyama J, Takahashi S, Paez MT, Nakagawa E, et al. TULIP1 (RALGAPA1) haploinsufficiency with brain development delay. Genomics. 2009;94:414–22.

    CAS  Article  Google Scholar 

  11. Tanaka M, Mino S, Ogura Y, Hayashi T, Sawabe T. Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: rumoiensis clade species as a test case. PeerJ. 2018;6:e5018.

    Article  Google Scholar 

  12. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34:2666–9.

    Article  Google Scholar 

  13. Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 2017;8:14061.

    CAS  Article  Google Scholar 

  14. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6:80–92.

    CAS  Article  Google Scholar 

  15. Inoue K, Osaka H, Sugiyama N, Kawanishi C, Onishi H, Nezu A, et al. A duplicated PLP gene causing Pelizaeus-Merzbacher disease detected by comparative multiplex PCR. Am J Hum Genet. 1996;59:32–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Inoue K, Osaka H, Imaizumi K, Nezu A, Takanashi J, Arii J, et al. Proteolipid protein gene duplications causing Pelizaeus-Merzbacher disease: molecular mechanism and phenotypic manifestations. Ann Neurol. 1999;45:624–32.

    CAS  Article  Google Scholar 

  17. Lee JA, Carvalho CM, Lupski JRA. DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell. 2007;131:1235–47.

    CAS  Article  Google Scholar 

  18. Zhang F, Khajavi M, Connolly AM, Towne CF, Batish SD, Lupski JR. The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet. 2009;41:849–53.

    CAS  Article  Google Scholar 

  19. Kato T, Ouchi Y, Inagaki H, Makita Y, Mizuno S, Kajita M, et al. Genomic characterization of chromosomal insertions: insights into the mechanisms underlying chromothripsis. Cytogenet Genome Res. 2017;153:1–9.

    Article  Google Scholar 

  20. Norris AL, Workman RE, Fan Y, Eshleman JR, Timp W. Nanopore sequencing detects structural variants in cancer. Cancer Biol Ther. 2016;17:246–53.

    CAS  Article  Google Scholar 

  21. Chatron N, Schluth-Bolard C, Fretigny M, Labalme A, Vilchez G, Castet SM, et al. Severe hemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing. J Thromb Haemost. 2019;17:1097–103.

    CAS  Article  Google Scholar 

  22. McGinty RJ, Rubinstein RG, Neil AJ, Dominska M, Kiktev D, Petes TD, et al. Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. Genome Res. 2017;27:2072–82.

    CAS  Article  Google Scholar 

  23. Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet. 2019;12:6.

    Article  Google Scholar 

  24. Maher CA, Wilson RK. Chromothripsis and human disease: piecing together the shattering process. Cell. 2012;148:29–32.

    CAS  Article  Google Scholar 

  25. Dazzo E, Fanciulli M, Serioli E, Minervini G, Pulitano P, Binelli S, et al. Heterozygous reelin mutations cause autosomal-dominant lateral temporal epilepsy. Am J Hum Genet. 2015;96:992–1000.

    CAS  Article  Google Scholar 

  26. Shen E, Shulha H, Weng Z, Akbarian S. Regulation of histone H3K4 methylation in brain development and disease. Philos Trans R Soc Lond B Biol Sci. 2014;369:20130514.

  27. O’Donnell-Luria AH, Pais LS, Faundes V, Wood JC, Sveden A, Luria V, et al. Heterozygous variants in KMT2E cause a spectrum of neurodevelopmental disorders and epilepsy. Am J Hum Genet. 2019;104:1210–22.

    Article  Google Scholar 

Download references


We would like to express our gratitude to the patient and her family for their cooperation. This work was supported by the Practical Research Project for Rare/Intractable Diseases (18ek0109270) and the Acceleration Program for Intractable Diseases Research utilizing Disease-specific iPS cells from Japan Agency for Medical Research and development (AMED), a Grant-in-Aid for Scientific Research from Health Labor Sciences Research Grants from the Ministry of Health, Labor and Welfare, Japan, and JSPS KAKENHI (TY). This work was also supported by a Grant-in-Aid for Young Scientists (B) (17K18133) and a Restart Postdoctoral Fellowship (17J40108) from the Japan Society for the Promotion of Science (JSPS) (KY-S). We are also thankful for the support from the Initiative on Rare and Undiagnosed Diseases (IRUD) via AMED.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Toshiyuki Yamamoto.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Imaizumi, T., Yamamoto-Shimojima, K., Yanagishita, T. et al. Analyses of breakpoint junctions of complex genomic rearrangements comprising multiple consecutive microdeletions by nanopore sequencing. J Hum Genet 65, 735–741 (2020).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


Quick links