{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T13:29:37Z","timestamp":1767965377813,"version":"3.49.0"},"reference-count":27,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2021,7,21]],"date-time":"2021-07-21T00:00:00Z","timestamp":1626825600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["1 NU88EH001323-01-00"],"award-info":[{"award-number":["1 NU88EH001323-01-00"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJNS"],"abstract":"<jats:p>Promising treatments for spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, prompted calls for inclusion in newborn screening (NBS). In January 2018, the New England Newborn Screening Program (NENSP) began statewide screening for SMA using a tiered algorithm looking for the absence of SMN1 Exon 7. When results from the first and second tier needed reconciliation, we developed and validated a third tier DNA sequencing assay to ensure the presence or absence of SMN1 Exon 7. All nine infants referred to specialty centers through NBS showed single base substitution of c.840C&gt;T, and were confirmed to have SMA. Further, a minor sequencing protocol modification allowed the estimation of SMN2 copy number in SMA affected patients; we developed and validated a copy-number assay yielding 100% match with seven previously characterized specimens of SMA patients. All nine SMA-affected infants found through NBS were also assayed for SMN2 copy number. Results were comparable but not 100% matched with those that were reported by independent diagnostic laboratories. In conclusion, a sequencing protocol confirms NBS findings from real-time qPCR, and its modified application allows NBS programs that have sequencing capabilities to provide SMN2 copy numbers without the need for additional instrumentation.<\/jats:p>","DOI":"10.3390\/ijns7030047","type":"journal-article","created":{"date-parts":[[2021,7,22]],"date-time":"2021-07-22T22:37:14Z","timestamp":1626993434000},"page":"47","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Novel Modification of a Confirmatory SMA Sequencing Assay that Can Be Used to Determine SMN2 Copy Number"],"prefix":"10.3390","volume":"7","author":[{"given":"Binod","family":"Kumar","sequence":"first","affiliation":[{"name":"New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA"},{"name":"Division of Genetics, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha","family":"Barton","sequence":"additional","affiliation":[{"name":"New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jolanta","family":"Kordowska","sequence":"additional","affiliation":[{"name":"New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roger B.","family":"Eaton","sequence":"additional","affiliation":[{"name":"New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA"},{"name":"Division of Genetics, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne M.","family":"Counihan","sequence":"additional","affiliation":[{"name":"New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaime E.","family":"Hale","sequence":"additional","affiliation":[{"name":"New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne Marie","family":"Comeau","sequence":"additional","affiliation":[{"name":"New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA"},{"name":"Division of Genetics, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,7,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.ncl.2015.07.004","article-title":"Spinal Muscular Atrophy","volume":"33","author":"Kolb","year":"2015","journal-title":"Neurol Clin."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1007\/s00439-002-0828-x","article-title":"Genetic testing and risk assessment for spinal muscular atrophy (SMA)","volume":"111","author":"Ogino","year":"2002","journal-title":"Hum. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1002\/(SICI)1098-1004(200003)15:3<228::AID-HUMU3>3.0.CO;2-9","article-title":"An update of the mutation spectrum of the survival motor neuron gene (SMN1) in autosomal recessive spinal muscular atrophy (SMA)","volume":"15","author":"Wirth","year":"2000","journal-title":"Hum. Mutat."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1111\/ahg.12031","article-title":"Spinal muscular atrophy: From gene discovery to clinical trials","volume":"77","author":"Nurputra","year":"2013","journal-title":"Ann. Hum. Genet."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1038\/sj.ejhg.5201288","article-title":"New insight on the evolution of the SMN1 and SMN2 region: Simulation and meta-analysis for allele and haplotype frequency calculations","volume":"12","author":"Ogino","year":"2004","journal-title":"Eur J. Hum. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1097\/00125817-200201000-00004","article-title":"Molecular analysis of spinal muscular atrophy and modification of the phenotype by SMN2","volume":"4","author":"Mailman","year":"2002","journal-title":"Genet. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1097\/GIM.0b013e318220d523","article-title":"Technical standards and guidelines for spinal muscular atrophy testing","volume":"13","author":"Prior","year":"2011","journal-title":"Genet. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1016\/j.ajhg.2009.08.002","article-title":"A positive modifier of spinal muscular atrophy in the SMN2 gene","volume":"85","author":"Prior","year":"2009","journal-title":"Am. J. Hum. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1016\/j.nmd.2018.01.003","article-title":"Correlation between SMA type and SMN2 copy number revisited: An analysis of 625 unrelated Spanish patients and a compilation of 2834 reported cases","volume":"28","author":"Calucho","year":"2018","journal-title":"Neuromuscular Disord."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1086\/338627","article-title":"Quantitative analyses of SMN1 and SMN2 based on real-time lightcycler PCR: Fast and highly reliable carrier testing and prediction of severity of spinal muscular atrophy","volume":"70","author":"Schwarzer","year":"2002","journal-title":"Am. J. Hum. Genet."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1373\/clinchem.2014.231019","article-title":"Newborn blood spot screening test using multiplexed real-time PCR to simultaneously screen for spinal muscular atrophy and severe combined immunodeficiency","volume":"61","author":"Taylor","year":"2015","journal-title":"Clin. Chem"},{"key":"ref_12","unstructured":"Lee, F.K. (2021, April 27). Newborn Screening for Spinal Muscular Atrophy (SMA) in the US. Presented at Spinal Muscular Atrophy: Overview 324 of Available Screening Methods, Webinar. Available online: https:\/\/www.newsteps.org\/sites\/default\/files\/re-325sources\/download\/aphl_sma_webinar_slides_webinarslides_june2018_kh.pdf."},{"key":"ref_13","unstructured":"Mercer, K. (2017, January 10\u201313). Newborn screening for spinal muscular atrophy. Proceedings of the Newborn Screening and Genetic Testing Sym-321 posium, New Orleans, LA, USA. Available online: https:\/\/www.aphl.org\/conferences\/proceedings\/Doc-322uments\/Mercer.pdf."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Hale, J.E., Darras, B.T., Swoboda, K.J., Estrella, E., Chen, J.Y.H., Abbott, M.A., Hay, B.N., Kumar, B., Counihan, A.M., and Gerstel-Thompson, J. (2021). Massachusetts\u2019 findings from statewide newborn screening for spinal muscular atrophy. Int J. Neonatal Screen., 23.","DOI":"10.3390\/ijns7020026"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.jns.2011.06.002","article-title":"Identification of bidirectional gene conversion between SMN1 and SMN2 by simultaneous analysis of SMN dosage and hybrid genes in a Chinese population","volume":"308","author":"Chen","year":"2011","journal-title":"J. Neurol Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/j.braindev.2020.09.005","article-title":"Clinical phenotypes of spinal muscular atrophy patients with hybrid SMN gene","volume":"43","author":"Niba","year":"2021","journal-title":"Brain Dev."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/hmg\/5.2.257","article-title":"Molecular analysis of the SMN and NAIP genes in Spanish spinal muscular atrophy (SMA) families and correlation between number of copies of c BCD541and SMA phenotype","volume":"5","author":"Velasco","year":"1996","journal-title":"Hum. Mol. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.jpeds.2017.06.042","article-title":"Presymptomatic Diagnosis of Spinal Muscular Atrophy Through Newborn Screening","volume":"190","author":"Chien","year":"2017","journal-title":"J. Pediatr."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1097\/GIM.0b013e31803d35bc","article-title":"Copy number analysis of survival motor neuron genes by multiplex ligation-dependent probe amplification","volume":"9","author":"Huang","year":"2007","journal-title":"Genet. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1373\/clinchem.2010.144915","article-title":"High-throughput multiplexed T-cell-receptor excision circle quantitative PCR assay with internal controls for detection of severe combined immunodeficiency in population-based newborn screening","volume":"56","author":"Wilkey","year":"2010","journal-title":"Clin. Chem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"97","DOI":"10.3233\/JND-190468","article-title":"Revised recommendations for the treatment of infants diagnosed with spinal muscular atrophy via newborn screening who have 4 copies of SMN2","volume":"7","author":"Glascock","year":"2020","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"145","DOI":"10.3233\/JND-180304","article-title":"Treatment algorithm for infants diagnosed with spinal muscular atrophy through newborn screening","volume":"5","author":"Glascock","year":"2018","journal-title":"J. Neuromuscul. Dis."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1212\/WNL.0000000000007836","article-title":"Discrepancy in redetermination of SMN2 copy numbers in children with SMA","volume":"93","author":"Schorling","year":"2019","journal-title":"Neurology"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1212\/WNL.0000000000009907","article-title":"Reader response: Discrepancy in redetermination of SMN2 copy numbers in children with SMA","volume":"95","author":"Dangouloff","year":"2020","journal-title":"Neurology"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1212\/WNL.0000000000009908","article-title":"Author response: Discrepancy in redetermination of SMN2 copy numbers in children with SMA","volume":"95","author":"Kirschner","year":"2020","journal-title":"Neurology"},{"key":"ref_26","first-page":"144","article-title":"Editors\u2019 note: Discrepancy in redetermination of SMN2 copy numbers in children with SMA","volume":"95","year":"2020","journal-title":"Neurology"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1002\/humu.24200","article-title":"Beyond copy number: A new, rapid, and versatile method for sequencing the entire SMN2 gene in SMA patients","volume":"42","author":"Paramonov","year":"2021","journal-title":"Hum. Mutat."}],"container-title":["International Journal of Neonatal Screening"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2409-515X\/7\/3\/47\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:32:46Z","timestamp":1760164366000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2409-515X\/7\/3\/47"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,21]]},"references-count":27,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2021,9]]}},"alternative-id":["ijns7030047"],"URL":"https:\/\/doi.org\/10.3390\/ijns7030047","relation":{},"ISSN":["2409-515X"],"issn-type":[{"value":"2409-515X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,21]]}}}