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Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

Abstract

Long-read sequencing technology is now capable of reading single-molecule DNA with an average read length of more than 10 kb, fully enabling the coverage of large structural variations (SVs). This advantage may pave the way for the detection of unprecedented SVs as well as repeat expansions. Pathogenic SVs of only known genes used to be selectively analyzed based on prior knowledge of target DNA sequence. The unbiased application of long-read whole-genome sequencing (WGS) for the detection of pathogenic SVs has just begun. Here, we apply PacBio SMRT sequencing in a Japanese family with benign adult familial myoclonus epilepsy (BAFME). Our SV selection of low-coverage WGS data (7×) narrowed down the candidates to only six SVs in a 7.16-Mb region of the BAFME1 locus and correctly determined an approximately 4.6-kb SAMD12 intronic repeat insertion, which is causal of BAFME1. These results indicate that long-read WGS is potentially useful for evaluating all of the known SVs in a genome and identifying new disease-causing SVs in combination with other genetic methods to resolve the genetic causes of currently unexplained diseases.

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References

  1. 1.

    Huddleston J, Chaisson MJ, Meltz Steinberg K, Warren W, Hoekzema K, Gordon DS, et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Res. 2016;27:677–85.

    Article  Google Scholar 

  2. 2.

    Seo JS, Rhie A, Kim J, Lee S, Sohn MH, Kim CU, et al. De novo assembly and phasing of a Korean human genome. Nature. 2016;538:243–7.

    CAS  Article  Google Scholar 

  3. 3.

    Miyatake S, Koshimizu E, Fujita A, Fukai R, Imagawa E, Ohba C, et al. Detecting copy-number variations in whole-exome sequencing data using the eXome Hidden Markov Model: an 'exome-first' approach. J Hum Genet. 2015;60:175–82.

    CAS  Article  Google Scholar 

  4. 4.

    Pirooznia M, Goes FS, Zandi PP. Whole-genome CNV analysis: advances in computational approaches. Front Genet. 2015;6:138.

    Article  Google Scholar 

  5. 5.

    Merker JD, Wenger AM, Sneddon T, Grove M, Zappala Z, Fresard L, et al. Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genet Med. 2018;20:159–63.

    CAS  Article  Google Scholar 

  6. 6.

    Reiner J, Pisani L, Qiao W, Singh R, Yang Y, Shi L, et al. Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet-Biedl Syndrome 9 (BBS9) deletion. NPJ Genom Med. 2018;3:3.

    Article  Google Scholar 

  7. 7.

    Ikeda A, Kakigi R, Funai N, Neshige R, Kuroda Y, Shibasaki H. Cortical tremor: a variant of cortical reflex myoclonus. Neurology. 1990;40:1561–5.

    CAS  Article  Google Scholar 

  8. 8.

    Inazuki G, Naito H, Ohama E, Kawase Y, Honma Y, Tokiguchi S, et al. [A clinical study and neuropathological findings of a familial disease with myoclonus and epilepsy—the nosological place of familial essential myoclonus and epilepsy (FEME)]. Seishin Shinkeigaku Zasshi—Psychiatr Et Neurol Jpn. 1990;92:1–21.

    CAS  Google Scholar 

  9. 9.

    Mikami M, Yasuda T, Terao A, Nakamura M, Ueno S, Tanabe H, et al. Localization of a gene for benign adult familial myoclonic epilepsy to chromosome 8q23.3-q24.1. Am J Hum Genet. 1999;65:745–51.

    CAS  Article  Google Scholar 

  10. 10.

    van Rootselaar AF, van Schaik IN, van den Maagdenberg AM, Koelman JH, Callenbach PM, Tijssen MA. Familial cortical myoclonic tremor with epilepsy: a single syndromic classification for a group of pedigrees bearing common features. Mov Disord. 2005;20:665–73.

    Article  Google Scholar 

  11. 11.

    Cen ZD, Xie F, Xiao JF, Luo W. Rational search for genes in familial cortical myoclonic tremor with epilepsy, clues from recent advances. Seizure. 2016;34:83–89.

    Article  Google Scholar 

  12. 12.

    Hitomi T, Kondo T, Kobayashi K, Matsumoto R, Takahashi R, Ikeda A. Clinical anticipation in Japanese families of benign adult familial myoclonus epilepsy. Epilepsia. 2012;53:e33–6.

    Article  Google Scholar 

  13. 13.

    Cen Z, Huang C, Yin H, Ding X, Xie F, Lu X, et al. Clinical and neurophysiological features of familial cortical myoclonic tremor with epilepsy. Mov Disord. 2016;31:1704–10.

    CAS  Article  Google Scholar 

  14. 14.

    Ishiura H, Doi K, Mitsui J, Yoshimura J, Matsukawa MK, Fujiyama A, et al. Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy. Nat Genet. 2018;50:581–90.

    CAS  Article  Google Scholar 

  15. 15.

    Cen Z, Jiang Z, Chen Y, Zheng X, Xie F, Yang X, et al. Intronic pentanucleotide TTTCA repeat insertion in the SAMD12 gene causes familial cortical myoclonic tremor with epilepsy type 1. Brain. 2018;141:2280–8.

    Article  Google Scholar 

  16. 16.

    Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res. 2018;46:2159–68.

    CAS  Article  Google Scholar 

  17. 17.

    Krumsiek J, Arnold R, Rattei T. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics. 2007;23:1026–8.

    CAS  Article  Google Scholar 

  18. 18.

    Carvalho CM, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet. 2016;17:224–38.

    CAS  Article  Google Scholar 

  19. 19.

    Hannan AJ. Tandem repeats mediating genetic plasticity in health and disease. Nat Rev Genet. 2018;19:286–98.

    CAS  Article  Google Scholar 

  20. 20.

    Doi K, Monjo T, Hoang PH, Yoshimura J, Yurino H, Mitsui J, et al. Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. Bioinformatics. 2014;30:815–22.

    CAS  Article  Google Scholar 

  21. 21.

    Dolzhenko E, van Vugt J, Shaw RJ, Bekritsky MA, van Blitterswijk M, Narzisi G, et al. Detection of long repeat expansions from PCR-free whole-genome sequence data. Genome Res. 2017;27:1895–903.

    CAS  Article  Google Scholar 

  22. 22.

    Tang H, Kirkness EF, Lippert C, Biggs WH, Fabani M, Guzman E, et al. Profiling of short-tandem-repeat disease alleles in 12,632 human whole genomes. Am J Hum Genet. 2017;101:700–15.

    CAS  Article  Google Scholar 

  23. 23.

    Dashnow H, Lek M, Phipson B, Halman A, Sadedin S, Lonsdale A, et al. STRetch: detecting and discovering pathogenic short tandem repeat expansions. Genome Biol. 2018;19:121.

    Article  Google Scholar 

  24. 24.

    McFarland KN, Liu J, Landrian I, Godiska R, Shanker S, Yu F, et al. SMRT sequencing of long tandem nucleotide repeats in SCA10 reveals unique insight of repeat expansion structure. PLoS ONE 2015;10:e0135906.

    Article  Google Scholar 

  25. 25.

    Schule B, McFarland KN, Lee K, Tsai YC, Nguyen KD, Sun C, et al. Parkinson’s disease associated with pure ATXN10 repeat expansion. NPJ Park Dis. 2017;3:27.

    Article  Google Scholar 

  26. 26.

    Höijer I, Tsai YC, Clark TA, Kotturi P, Dahl N, Stattin EL, et al. Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing. Hum Mutat. 2018;39:1262–72.

    Article  Google Scholar 

  27. 27.

    Mirkin SM. DNA structures, repeat expansions and human hereditary disorders. Curr Opin Struct Biol. 2006;16:351–8.

    CAS  Article  Google Scholar 

  28. 28.

    Landrian I, McFarland KN, Liu J, Mulligan CJ, Rasmussen A, Ashizawa T. Inheritance patterns of ATCCT repeat interruptions in spinocerebellar ataxia type 10 (SCA10) expansions. PLoS ONE 2017;12:e0175958.

    Article  Google Scholar 

  29. 29.

    Usdin K, House NC, Freudenreich CH. Repeat instability during DNA repair: Insights from model systems. Crit Rev Biochem Mol Biol. 2015;50:142–67.

    CAS  Article  Google Scholar 

  30. 30.

    Mori S, Nakamura M, Yasuda T, Ueno S, Kaneko S, Sano A. Remapping and mutation analysis of benign adult familial myoclonic epilepsy in a Japanese pedigree. J Hum Genet. 2011;56:742–7.

    CAS  Article  Google Scholar 

  31. 31.

    English AC, Salerno WJ, Reid JG. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinform. 2014;15:180.

    Article  Google Scholar 

  32. 32.

    Fang L, Hu J, Wang D, Wang K. NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data. BMC Bioinform. 2018;19:180.

    Article  Google Scholar 

  33. 33.

    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 

  34. 34.

    Zeng S, Zhang MY, Wang XJ, Hu ZM, Li JC, Li N, et al. Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy. Journal of medical genetics 2018. https://doi.org/10.1136/jmedgenet-2018-105484.

    Article  Google Scholar 

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Acknowledgements

We would like to thank all of the subjects for participating in this study. We also thank N. Watanabe, T. Miyama, M. Sato, and K. Takabe for their technical assistance and A. Wenger (Pacific Biosciences) for helpful comments. We are also grateful to Edanz Group (www.edanzediting.com/ac) for editing a draft of this manuscript. This work was supported by AMED under grant numbers JP18ek0109280, JP18dm0107090, JP18ek0109301, JP18ek0109348, and JP18kk020500; by JSPS KAKENHI under grant numbers JP17K15630, JP17H01539, JP17K10080, and JP17K15630; by JST under the Creation of Innovation Centers for Advanced Interdisciplinary Research Areas Program in the Project for Developing Innovation Systems; the Ministry of Health, Labor, and Welfare; and Takeda Science Foundation.

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Correspondence to Takeshi Mizuguchi or Satoko Miyatake.

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Mizuguchi, T., Toyota, T., Adachi, H. et al. Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases. J Hum Genet 64, 191–197 (2019). https://doi.org/10.1038/s10038-018-0551-7

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