Abstract
Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality. Homozygous deletion of Survival Motor Neuron (SMN) 1 causes the disease in 95% of cases, but severity varies with the copy number of SMN2. The nearly identical sequences of the SMN genes make differentiation between them difficult, and current methodologies such as multiplex ligation-dependent probe amplification (MLPA) and real-time PCR (RT-PCR) present limitations for diagnosis. In this report, we analyse SMA samples of known copy number to compare new emerging technologies (Linked-Reads, Cytoscan array and next generation sequencing) against MLPA. MLPA analysis was the only method able to report the known copy numbers of the samples, making it still the most reliable means of SMA carrier screening and diagnosis. However, the three new methodologies are still emerging technologies for routine diagnostics compared to MLPA, and with further optimisation, they could greatly improve SMA carrier screening and diagnosis.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
MedlinePlus (2020). SMN1 gene—survival of motor neuron 1, telomeric. U.S. National Library of Medicine. https://medlineplus.gov/genetics/gene/smn1/
Prior, T. W., Nagan, N., Sugarman, E. A., Batish, S. D., & Braastad, C. (2011). Technical standards and guidelines for spinal muscular atrophy testing. Genetics in Medicine, 13(7), 686–694. https://doi.org/10.1097/GIM.0b013e318220d523
Jones, K., & Livingston, A. (2019). Spinal Muscular Atrophy and the Difficult SMN1 Gene. https://www.thermofisher.com/blog/behindthebench/spinal-muscular-atrophy-and-the-difficult-smn1-gene/
National Center for Biotechnology Information (NCBI) (2020, December 6). SMN1 survival of motor neuron 1, telomeric [Homo sapiens (human)]. U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/gene/6606
Monani, U. R., Lorson, C. L., Parsons, D. W., Prior, T. W., Androphy, E. J., Burghes, A. H. M., & McPherson, J. D. (1999). A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2. Human Molecular Genetics, 8(7), 1177–1183. https://doi.org/10.1093/hmg/8.7.1177
Chen, X., Sanchis-Juan, A., French, C. E., Connell, A. J., Delon, I., Kingsbury, Z., Chawla, A., Halpern, A. L., Taft, R. J., Bentley, D. R., Butchbach, M. E. R., Raymond, F. L., Eberle, M. A., & BioResource, N. I. H. R. (2020). Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genetics in Medicine, 22(5), 945–953. https://doi.org/10.1038/s41436-020-0754-0
Zhang, L., Zhou, X., Weng, Z., & Sidow, A. (2019). Assessment of human diploid genome assembly with 10× linked-reads data. GigaScience, 8(giz141). https://doi.org/10.1093/gigascience/giz141
Thermo Fisher Scientific Inc. (2020). Chromosome analysis suite (ChAS) v4.2. https://assets.thermofisher.com/TFS-Assets/GSD/Handbooks/ChAS_4.2_Manual.pdf
MRC-Holland. (n.d.). Principle of MLPA. https://www.mrcholland.com/technology/mlpa/technique
Ogino, S., Gao, S., Leonard, D. G. B., Paessler, M., & Wilson, R. B. (2003). Inverse correlation between SMN1 and SMN2 copy numbers: Evidence for gene conversion from SMN2 to SMN1. European Journal of Human Genetics, 11(3), 275–277. https://doi.org/10.1038/sj.ejhg.5200957
Tattini, L., D’Aurizio, R., & Magi, A. (2015). Detection of genomic structural variants from next-generation sequencing data. Frontiers in Bioengineering and Biotechnology, 3, 92. https://doi.org/10.3389/fbioe.2015.00092
Chen, Z., Pham, L., Wu, T.-C., Mo, G., Xia, Y., Chang, P., Porter, D., Phan, T., Che, H., Tran, H., Bansal, V., Shaffer, J., Belda-Ferre, P., Humphrey, G., Knight, R., Pevzner, P., Pham, S., Wang, Y., & Lei, M. (2019). Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing. BioRxiv, 852947.https://doi.org/10.1101/852947
Ott, A., Schnable, J. C., Yeh, C.-T., Wu, L., Liu, C., Hu, H.-C., Dalgard, C. L., Sarkar, S.
Berkner, S., & Lipps, G. (2007). An active nonautonomous mobile element in Sulfolobus islandicus REN1H1. Journal of Bacteriology, 189(5), 2145–2149. https://doi.org/10.1128/JB.01567-06
10x Genomics. (n.d.). What is the difference between a phase set in the long ranger VCF and a phase block in the loupe browser? https://kb.10xgenomics.com/hc/en-us/articles/360001336291-What-is-the-difference-between-a-phase-set-in-the-Long-Ranger-VCF-and-a-phase-block-in-the-Loupe-Browser
Mandelker, D., Schmidt, R. J., Ankala, A., McDonald Gibson, K., Bowser, M., Sharma, H., Duffy, E., Hegde, M., Santani, A., Lebo, M., & Funke, B. (2016). Navigating highly homologous genes in a molecular diagnostic setting: A resource for clinical next-generation sequencing. Genetics in Medicine, 18(12), 1282–1289. https://doi.org/10.1038/gim.2016.58
Nature Education (2014). Microarray. https://www.nature.com/scitable/definition/microarray-202/
Lutgen, D., Ritter, R., Olsen, R.-A., Schielzeth, H., Gruselius, J., Ewels, P., García, J.T., Shirihai, H., Schweizer, M., Suh, A., Burri, R. (2020). Linked‐read sequencing enables haplotype‐resolved resequencing at population scale. https://doi.org/10.1111/1755-0998.13192
Chouvarine, P., Wiehlmann, L., Losada, P. M., DeLuca, D. S., & Tümmler, B. (2016). Filtration and normalization of sequencing read data in whole-metagenome shotgun samples. PLoS ONE, 11(10), e0165015. https://doi.org/10.1371/journal.pone.0165015
Ruhno, C., McGovern, V. L., Avenarius, M. R., Snyder, P. J., Prior, T. W., Nery, F. C., Muhtaseb, A., Roggenbuck, J. S., Kissel, J. T., Sansone, V. A., Siranosian, J. J., Johnstone, A. J., Nwe, P. H., Zhang, R. Z., Swoboda, K. J., & Burghes, A. (2019). Complete sequencing of the SMN2 gene in SMA patients detects SMN gene deletion junctions and variants in SMN2 that modify the SMA phenotype. Human Genetics, 138(3), 241–256. https://doi.org/10.1007/s00439-019-01983-0
Acknowledgements
We would like to thank Professor Lai Poh San, Dr Liu Chun Ping and Ms Grace Tan Li Xuan from the Department of Paediatrics for their guidance and National University Singapore (NUS) for the valuable learning opportunity.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this paper
Cite this paper
Sim, J., Xie, J., Tan, G.L.X., Liu, C.P., Lai, P.S. (2022). Spinal Muscular Atrophy: Evaluation of New Emerging Methods for Carrier Screening and Diagnosis. In: Guo, H., Ren, H., Wang, V., Chekole, E.G., Lakshmanan, U. (eds) IRC-SET 2021. Springer, Singapore. https://doi.org/10.1007/978-981-16-9869-9_1
Download citation
DOI: https://doi.org/10.1007/978-981-16-9869-9_1
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-16-9868-2
Online ISBN: 978-981-16-9869-9
eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)