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

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

doi:10.1007/s00439-019-01983-0

Original Investigation
Published: 20 February 2019

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

Corey Ruhno¹,
Vicki L. McGovern¹,
Matthew R. Avenarius²,
Pamela J. Snyder³,
Thomas W. Prior⁴,
Flavia C. Nery⁵,
Abdurrahman Muhtaseb⁵,
Jennifer S. Roggenbuck⁶,
John T. Kissel⁶,
Valeria A. Sansone⁷,
Jennifer J. Siranosian⁵,
Alec J. Johnstone⁵,
Pann H. Nwe⁵,
Ren Z. Zhang⁵,
Kathryn J. Swoboda⁵ &
Arthur H. M. Burghes¹

Human Genetics volume 138, pages 241–256 (2019)Cite this article

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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.

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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.

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Corey Ruhno and Vicki L. McGovern contributed equally to this work.

Affiliations

Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
Corey Ruhno, Vicki L. McGovern & Arthur H. M. Burghes
Nationwide Children’s Hospital, Columbus, OH, USA
Matthew R. Avenarius
Department of Pathology, The Ohio State University, Columbus, OH, USA
Pamela J. Snyder
Department of Pathology, Case Western Reserve Medical Center, Cleveland, OH, USA
Thomas W. Prior
Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
Flavia C. Nery, Abdurrahman Muhtaseb, Jennifer J. Siranosian, Alec J. Johnstone, Pann H. Nwe, Ren Z. Zhang & Kathryn J. Swoboda
Department of Neurology, The Ohio State University, Columbus, OH, USA
Jennifer S. Roggenbuck & John T. Kissel
The NEMO Clinical Center, University of Milan, Milan, Italy
Valeria A. Sansone

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

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Ruhno, C., McGovern, V.L., Avenarius, M.R. et al. Complete sequencing of the SMN2 gene in SMA patients detects SMN gene deletion junctions and variants in SMN2 that modify the SMA phenotype. Hum Genet 138, 241–256 (2019). https://doi.org/10.1007/s00439-019-01983-0

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Received: 20 November 2018
Accepted: 14 February 2019
Published: 20 February 2019
Issue Date: 04 March 2019
DOI: https://doi.org/10.1007/s00439-019-01983-0

Keywords

SMA
SMN1
SMN2
Deletion
Modifier