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Human Genetics

, Volume 138, Issue 3, pp 241–256 | Cite as

Complete sequencing of the SMN2 gene in SMA patients detects SMN gene deletion junctions and variants in SMN2 that modify the SMA phenotype

  • Corey Ruhno
  • Vicki L. McGovern
  • Matthew R. Avenarius
  • Pamela J. Snyder
  • Thomas W. Prior
  • Flavia C. Nery
  • Abdurrahman Muhtaseb
  • Jennifer S. Roggenbuck
  • John T. Kissel
  • Valeria A. Sansone
  • Jennifer J. Siranosian
  • Alec J. Johnstone
  • Pann H. Nwe
  • Ren Z. Zhang
  • Kathryn J. Swoboda
  • Arthur H. M. BurghesEmail author
Original Investigation
  • 299 Downloads

Abstract

Spinal muscular atrophy (SMA) is a progressive motor neuron disease caused by loss or mutation of the survival motor neuron 1 (SMN1) gene and retention of SMN2. We performed targeted capture and sequencing of the SMN2, CFTR, and PLS3 genes in 217 SMA patients. We identified a 6.3 kilobase deletion that occurred in both SMN1 and SMN2 (SMN1/2) and removed exons 7 and 8. The deletion junction was flanked by a 21 bp repeat that occurred 15 times in the SMN1/2 gene. We screened for its presence in 466 individuals with the known SMN1 and SMN2 copy numbers. In individuals with 1 SMN1 and 0 SMN2 copies, the deletion occurred in 63% of cases. We modeled the deletion junction frequency and determined that the deletion occurred in both SMN1 and SMN2. We have identified the first deletion junction where the deletion removes exons 7 and 8 of SMN1/2. As it occurred in SMN1, it is a pathogenic mutation. We called variants in the PLS3 and SMN2 genes, and tested for association with mild or severe exception patients. The variants A-44G, A-549G, and C-1897T in intron 6 of SMN2 were significantly associated with mild exception patients, but no PLS3 variants correlated with severity. The variants occurred in 14 out of 58 of our mild exception patients, indicating that mild exception patients with an intact SMN2 gene and without modifying variants occur. This sample set can be used in the association analysis of candidate genes outside of SMN2 that modify the SMA phenotype.

Keywords

SMA SMN1 SMN2 Deletion Modifier 

Notes

Acknowledgements

These studies were supported by a grant from the Muscular Dystrophy Association MDA352913. In addition, funding was provided from the National Institutes of Child Health and Development (NICHD) R01HD069045 Award to KJS for development of the Project Cure SMA Longitudinal Pediatric Data Repository. Corey Ruhno was supported by NICHD grant HD060586. We would also like to thank the Ohio Supercomputing Center. Anton J. Blatnik III assisted with sequencing of polymorphic markers. Finally, thank you to Dr. Jennifer Sinnott in The Ohio State University Department of Statistics for assisting us with the development of the models used in this paper.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

439_2019_1983_MOESM1_ESM.xlsx (104 kb)
Supplementary material 1 (XLSX 103 KB)
439_2019_1983_MOESM2_ESM.xlsx (14 kb)
Supplementary material 1 (XLSX 13 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Corey Ruhno
    • 1
  • Vicki L. McGovern
    • 1
  • Matthew R. Avenarius
    • 2
  • Pamela J. Snyder
    • 3
  • Thomas W. Prior
    • 4
  • Flavia C. Nery
    • 5
  • Abdurrahman Muhtaseb
    • 5
  • Jennifer S. Roggenbuck
    • 6
  • John T. Kissel
    • 6
  • Valeria A. Sansone
    • 7
  • Jennifer J. Siranosian
    • 5
  • Alec J. Johnstone
    • 5
  • Pann H. Nwe
    • 5
  • Ren Z. Zhang
    • 5
  • Kathryn J. Swoboda
    • 5
  • Arthur H. M. Burghes
    • 1
    Email author
  1. 1.Department of Biological Chemistry and PharmacologyThe Ohio State UniversityColumbusUSA
  2. 2.Nationwide Children’s HospitalColumbusUSA
  3. 3.Department of PathologyThe Ohio State UniversityColumbusUSA
  4. 4.Department of PathologyCase Western Reserve Medical CenterClevelandUSA
  5. 5.Department of Neurology, Center for Genomic MedicineMassachusetts General HospitalBostonUSA
  6. 6.Department of NeurologyThe Ohio State UniversityColumbusUSA
  7. 7.The NEMO Clinical CenterUniversity of MilanMilanItaly

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