Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy

M M Zwartkruis; M G Elferink; D Gommers; I Signoria; L Blasco-Pérez; M Costa-Roger; J van der Sel; I J Renkens; J W Green; J V Kortooms; C Vermeulen; R Straver; H W M van Deutekom; J H Veldink; F Asselman; E F Tizzano; R I Wadman; W L van der Pol; G W van Haaften; E J N Groen

doi:10.1186/s13073-025-01448-2

Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy

M M Zwartkruis, M G Elferink, D Gommers, I Signoria, L Blasco-Pérez, M Costa-Roger, J van der Sel, I J Renkens, J W Green, J V Kortooms, C Vermeulen, R Straver, H W M van Deutekom, J H Veldink, F Asselman, E F Tizzano, R I Wadman, W L van der Pol, G W van Haaften, E J N Groen

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

BACKGROUND: The complex 2 Mb survival motor neuron (SMN) locus on chromosome 5q13, including the spinal muscular atrophy (SMA)-causing gene SMN1 and modifier SMN2, remains incompletely resolved due to numerous segmental duplications. Variation in SMN2 copy number, presumably influenced by SMN1 to SMN2 gene conversion, affects disease severity, though SMN2 copy number alone has insufficient prognostic value due to limited genotype-phenotype correlations. With advancements in newborn screening and SMN-targeted therapies, identifying genetic markers to predict disease progression and treatment response is crucial. Progress has thus far been limited by methodological constraints.

METHODS: To address this, we developed HapSMA, a method to perform polyploid phasing of the SMN locus to enable copy-specific analysis of SMN and its surrounding genes. We used HapSMA on publicly available Oxford Nanopore Technologies (ONT) sequencing data of 29 healthy controls and performed long-read, targeted ONT sequencing of the SMN locus of 31 patients with SMA.

RESULTS: In healthy controls, we identified single nucleotide variants (SNVs) specific to SMN1 and SMN2 haplotypes that could serve as gene conversion markers. Broad phasing including the NAIP gene allowed for a more complete view of SMN locus variation. Genetic variation in SMN2 haplotypes was larger in SMA patients. Forty-two percent of SMN2 haplotypes of SMA patients showed varying SMN1 to SMN2 gene conversion breakpoints, serving as direct evidence of gene conversion as a common genetic characteristic in SMA and highlighting the importance of inclusion of SMA patients when investigating the SMN locus.

CONCLUSIONS: Our findings illustrate that both methodological advances and the analysis of patient samples are required to advance our understanding of complex genetic loci and address critical clinical challenges.

Original language	English
Article number	26
Journal	Genome Medicine
Volume	17
Issue number	1
DOIs	https://doi.org/10.1186/s13073-025-01448-2
Publication status	Published - 21 Mar 2025

Keywords

Dark genomic regions
Gene conversion
Long-read sequencing
Segmental duplications
Spinal muscular atrophy

Access to Document

10.1186/s13073-025-01448-2Licence: CC BY

s13073-025-01448-2Final published version, 2.15 MBLicence: CC BY

Cite this

Zwartkruis, M. M., Elferink, M. G., Gommers, D., Signoria, I., Blasco-Pérez, L., Costa-Roger, M., van der Sel, J., Renkens, I. J., Green, J. W., Kortooms, J. V., Vermeulen, C., Straver, R., van Deutekom, H. W. M., Veldink, J. H., Asselman, F., Tizzano, E. F., Wadman, R. I., van der Pol, W. L., van Haaften, G. W., & Groen, E. J. N. (2025). Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy. Genome Medicine, 17(1), Article 26. https://doi.org/10.1186/s13073-025-01448-2

@article{6dddd13f8d0d4a8b9386c9a2ff6ab518,

title = "Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy",

abstract = "BACKGROUND: The complex 2 Mb survival motor neuron (SMN) locus on chromosome 5q13, including the spinal muscular atrophy (SMA)-causing gene SMN1 and modifier SMN2, remains incompletely resolved due to numerous segmental duplications. Variation in SMN2 copy number, presumably influenced by SMN1 to SMN2 gene conversion, affects disease severity, though SMN2 copy number alone has insufficient prognostic value due to limited genotype-phenotype correlations. With advancements in newborn screening and SMN-targeted therapies, identifying genetic markers to predict disease progression and treatment response is crucial. Progress has thus far been limited by methodological constraints.METHODS: To address this, we developed HapSMA, a method to perform polyploid phasing of the SMN locus to enable copy-specific analysis of SMN and its surrounding genes. We used HapSMA on publicly available Oxford Nanopore Technologies (ONT) sequencing data of 29 healthy controls and performed long-read, targeted ONT sequencing of the SMN locus of 31 patients with SMA.RESULTS: In healthy controls, we identified single nucleotide variants (SNVs) specific to SMN1 and SMN2 haplotypes that could serve as gene conversion markers. Broad phasing including the NAIP gene allowed for a more complete view of SMN locus variation. Genetic variation in SMN2 haplotypes was larger in SMA patients. Forty-two percent of SMN2 haplotypes of SMA patients showed varying SMN1 to SMN2 gene conversion breakpoints, serving as direct evidence of gene conversion as a common genetic characteristic in SMA and highlighting the importance of inclusion of SMA patients when investigating the SMN locus.CONCLUSIONS: Our findings illustrate that both methodological advances and the analysis of patient samples are required to advance our understanding of complex genetic loci and address critical clinical challenges.",

keywords = "Dark genomic regions, Gene conversion, Long-read sequencing, Segmental duplications, Spinal muscular atrophy",

author = "Zwartkruis, {M M} and Elferink, {M G} and D Gommers and I Signoria and L Blasco-P{\'e}rez and M Costa-Roger and {van der Sel}, J and Renkens, {I J} and Green, {J W} and Kortooms, {J V} and C Vermeulen and R Straver and {van Deutekom}, {H W M} and Veldink, {J H} and F Asselman and Tizzano, {E F} and Wadman, {R I} and {van der Pol}, {W L} and {van Haaften}, {G W} and Groen, {E J N}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = mar,

day = "21",

doi = "10.1186/s13073-025-01448-2",

language = "English",

volume = "17",

journal = "Genome Medicine",

issn = "1756-994x",

publisher = "BioMed Central",

number = "1",

}

Zwartkruis, MM, Elferink, MG, Gommers, D, Signoria, I, Blasco-Pérez, L, Costa-Roger, M, van der Sel, J, Renkens, IJ, Green, JW, Kortooms, JV, Vermeulen, C, Straver, R, van Deutekom, HWM , Veldink, JH, Asselman, F, Tizzano, EF, Wadman, RI, van der Pol, WL , van Haaften, GW & Groen, EJN 2025, 'Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy', Genome Medicine, vol. 17, no. 1, 26. https://doi.org/10.1186/s13073-025-01448-2

TY - JOUR

T1 - Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy

AU - Zwartkruis, M M

AU - Elferink, M G

AU - Gommers, D

AU - Signoria, I

AU - Blasco-Pérez, L

AU - Costa-Roger, M

AU - van der Sel, J

AU - Renkens, I J

AU - Green, J W

AU - Kortooms, J V

AU - Vermeulen, C

AU - Straver, R

AU - van Deutekom, H W M

AU - Veldink, J H

AU - Asselman, F

AU - Tizzano, E F

AU - Wadman, R I

AU - van der Pol, W L

AU - van Haaften, G W

AU - Groen, E J N

PY - 2025/3/21

Y1 - 2025/3/21

N2 - BACKGROUND: The complex 2 Mb survival motor neuron (SMN) locus on chromosome 5q13, including the spinal muscular atrophy (SMA)-causing gene SMN1 and modifier SMN2, remains incompletely resolved due to numerous segmental duplications. Variation in SMN2 copy number, presumably influenced by SMN1 to SMN2 gene conversion, affects disease severity, though SMN2 copy number alone has insufficient prognostic value due to limited genotype-phenotype correlations. With advancements in newborn screening and SMN-targeted therapies, identifying genetic markers to predict disease progression and treatment response is crucial. Progress has thus far been limited by methodological constraints.METHODS: To address this, we developed HapSMA, a method to perform polyploid phasing of the SMN locus to enable copy-specific analysis of SMN and its surrounding genes. We used HapSMA on publicly available Oxford Nanopore Technologies (ONT) sequencing data of 29 healthy controls and performed long-read, targeted ONT sequencing of the SMN locus of 31 patients with SMA.RESULTS: In healthy controls, we identified single nucleotide variants (SNVs) specific to SMN1 and SMN2 haplotypes that could serve as gene conversion markers. Broad phasing including the NAIP gene allowed for a more complete view of SMN locus variation. Genetic variation in SMN2 haplotypes was larger in SMA patients. Forty-two percent of SMN2 haplotypes of SMA patients showed varying SMN1 to SMN2 gene conversion breakpoints, serving as direct evidence of gene conversion as a common genetic characteristic in SMA and highlighting the importance of inclusion of SMA patients when investigating the SMN locus.CONCLUSIONS: Our findings illustrate that both methodological advances and the analysis of patient samples are required to advance our understanding of complex genetic loci and address critical clinical challenges.

AB - BACKGROUND: The complex 2 Mb survival motor neuron (SMN) locus on chromosome 5q13, including the spinal muscular atrophy (SMA)-causing gene SMN1 and modifier SMN2, remains incompletely resolved due to numerous segmental duplications. Variation in SMN2 copy number, presumably influenced by SMN1 to SMN2 gene conversion, affects disease severity, though SMN2 copy number alone has insufficient prognostic value due to limited genotype-phenotype correlations. With advancements in newborn screening and SMN-targeted therapies, identifying genetic markers to predict disease progression and treatment response is crucial. Progress has thus far been limited by methodological constraints.METHODS: To address this, we developed HapSMA, a method to perform polyploid phasing of the SMN locus to enable copy-specific analysis of SMN and its surrounding genes. We used HapSMA on publicly available Oxford Nanopore Technologies (ONT) sequencing data of 29 healthy controls and performed long-read, targeted ONT sequencing of the SMN locus of 31 patients with SMA.RESULTS: In healthy controls, we identified single nucleotide variants (SNVs) specific to SMN1 and SMN2 haplotypes that could serve as gene conversion markers. Broad phasing including the NAIP gene allowed for a more complete view of SMN locus variation. Genetic variation in SMN2 haplotypes was larger in SMA patients. Forty-two percent of SMN2 haplotypes of SMA patients showed varying SMN1 to SMN2 gene conversion breakpoints, serving as direct evidence of gene conversion as a common genetic characteristic in SMA and highlighting the importance of inclusion of SMA patients when investigating the SMN locus.CONCLUSIONS: Our findings illustrate that both methodological advances and the analysis of patient samples are required to advance our understanding of complex genetic loci and address critical clinical challenges.

KW - Dark genomic regions

KW - Gene conversion

KW - Long-read sequencing

KW - Segmental duplications

KW - Spinal muscular atrophy

UR - http://www.scopus.com/inward/record.url?scp=105000478009&partnerID=8YFLogxK

U2 - 10.1186/s13073-025-01448-2

DO - 10.1186/s13073-025-01448-2

M3 - Article

C2 - 40119448

SN - 1756-994x

VL - 17

JO - Genome Medicine

JF - Genome Medicine

IS - 1

M1 - 26

ER -

Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this