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American Journal of Human Genetics logoLink to American Journal of Human Genetics
. 1997 Jun;60(6):1411–1422. doi: 10.1086/515465

Identification of proximal spinal muscular atrophy carriers and patients by analysis of SMNT and SMNC gene copy number.

P E McAndrew 1, D W Parsons 1, L R Simard 1, C Rochette 1, P N Ray 1, J R Mendell 1, T W Prior 1, A H Burghes 1
PMCID: PMC1716150  PMID: 9199562

Abstract

The survival motor neuron (SMN) transcript is encoded by two genes, SMNT and SMNC. The autosomal recessive proximal spinal muscular atrophy that maps to 5q12 is caused by mutations in the SMNT gene. The SMNT gene can be distinguished from the SMNC gene by base-pair changes in exons 7 and 8. SMNT exon 7 is not detected in approximately 95% of SMA cases due to either deletion or sequence-conversion events. Small mutations in SMNT now have been identified in some of the remaining nondeletion patients. However, there is no reliable quantitative assay for SMNT, to distinguish SMA compound heterozygotes from non-5q SMA-like cases (phenocopies) and to accurately determine carrier status. We have developed a quantitative PCR assay for the determination of SMNT and SMNC gene-copy number. This report demonstrates how risk estimates for the diagnosis and detection of SMA carriers can be modified by the accurate determination of SMNT copy number.

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Selected References

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  1. Brahe C., Clermont O., Zappata S., Tiziano F., Melki J., Neri G. Frameshift mutation in the survival motor neuron gene in a severe case of SMA type I. Hum Mol Genet. 1996 Dec;5(12):1971–1976. doi: 10.1093/hmg/5.12.1971. [DOI] [PubMed] [Google Scholar]
  2. Brahe C., Velonà I., van der Steege G., Zappata S., van de Veen A. Y., Osinga J., Tops C. M., Fodde R., Khan P. M., Buys C. H. Mapping of two new markers within the smallest interval harboring the spinal muscular atrophy locus by family and radiation hybrid analysis. Hum Genet. 1994 May;93(5):494–501. doi: 10.1007/BF00202811. [DOI] [PubMed] [Google Scholar]
  3. Brzustowicz L. M., Lehner T., Castilla L. H., Penchaszadeh G. K., Wilhelmsen K. C., Daniels R., Davies K. E., Leppert M., Ziter F., Wood D. Genetic mapping of chronic childhood-onset spinal muscular atrophy to chromosome 5q11.2-13.3. Nature. 1990 Apr 5;344(6266):540–541. doi: 10.1038/344540a0. [DOI] [PubMed] [Google Scholar]
  4. Burghes A. H., Ingraham S. E., Kóte-Jarai Z., Rosenfeld S., Herta N., Nadkarni N., DiDonato C. J., Carpten J., Hurko O., Florence J. Linkage mapping of the spinal muscular atrophy gene. Hum Genet. 1994 Mar;93(3):305–312. doi: 10.1007/BF00212028. [DOI] [PubMed] [Google Scholar]
  5. Burghes A. H., Ingraham S. E., McLean M., Thompson T. G., McPherson J. D., Kote-Jarai Z., Carpten J. D., DiDonato C. J., Ikeda J. E., Surh L. A multicopy dinucleotide marker that maps close to the spinal muscular atrophy gene. Genomics. 1994 May 15;21(2):394–402. doi: 10.1006/geno.1994.1282. [DOI] [PubMed] [Google Scholar]
  6. Bussaglia E., Clermont O., Tizzano E., Lefebvre S., Bürglen L., Cruaud C., Urtizberea J. A., Colomer J., Munnich A., Baiget M. A frame-shift deletion in the survival motor neuron gene in Spanish spinal muscular atrophy patients. Nat Genet. 1995 Nov;11(3):335–337. doi: 10.1038/ng1195-335. [DOI] [PubMed] [Google Scholar]
  7. Bürglen L., Lefebvre S., Clermont O., Burlet P., Viollet L., Cruaud C., Munnich A., Melki J. Structure and organization of the human survival motor neurone (SMN) gene. Genomics. 1996 Mar 15;32(3):479–482. doi: 10.1006/geno.1996.0147. [DOI] [PubMed] [Google Scholar]
  8. Carpten J. D., DiDonato C. J., Ingraham S. E., Wagner-McPherson C., Nieuwenhuijsen B. W., Wasmuth J. J., Burghes A. H. A YAC contig of the region containing the spinal muscular atrophy gene (SMA): identification of an unstable region. Genomics. 1994 Nov 15;24(2):351–356. doi: 10.1006/geno.1994.1626. [DOI] [PubMed] [Google Scholar]
  9. Celi F. S., Cohen M. M., Antonarakis S. E., Wertheimer E., Roth J., Shuldiner A. R. Determination of gene dosage by a quantitative adaptation of the polymerase chain reaction (gd-PCR): rapid detection of deletions and duplications of gene sequences. Genomics. 1994 May 15;21(2):304–310. doi: 10.1006/geno.1994.1270. [DOI] [PubMed] [Google Scholar]
  10. Celi F. S., Zenilman M. E., Shuldiner A. R. A rapid and versatile method to synthesize internal standards for competitive PCR. Nucleic Acids Res. 1993 Feb 25;21(4):1047–1047. doi: 10.1093/nar/21.4.1047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cobben J. M., van der Steege G., Grootscholten P., de Visser M., Scheffer H., Buys C. H. Deletions of the survival motor neuron gene in unaffected siblings of patients with spinal muscular atrophy. Am J Hum Genet. 1995 Oct;57(4):805–808. [PMC free article] [PubMed] [Google Scholar]
  12. DiDonato C. J., Chen X. N., Noya D., Korenberg J. R., Nadeau J. H., Simard L. R. Cloning, characterization, and copy number of the murine survival motor neuron gene: homolog of the spinal muscular atrophy-determining gene. Genome Res. 1997 Apr;7(4):339–352. doi: 10.1101/gr.7.4.339. [DOI] [PubMed] [Google Scholar]
  13. DiDonato C. J., Ingraham S. E., Mendell J. R., Prior T. W., Lenard S., Moxley R. T., 3rd, Florence J., Burghes A. H. Deletion and conversion in spinal muscular atrophy patients: is there a relationship to severity? Ann Neurol. 1997 Feb;41(2):230–237. doi: 10.1002/ana.410410214. [DOI] [PubMed] [Google Scholar]
  14. DiDonato C. J., Morgan K., Carpten J. D., Fuerst P., Ingraham S. E., Prescott G., McPherson J. D., Wirth B., Zerres K., Hurko O. Association between Ag1-CA alleles and severity of autosomal recessive proximal spinal muscular atrophy. Am J Hum Genet. 1994 Dec;55(6):1218–1229. [PMC free article] [PubMed] [Google Scholar]
  15. Francis M. J., Morrison K. E., Campbell L., Grewal P. K., Christodoulou Z., Daniels R. J., Monaco A. P., Frischauf A. M., McPherson J., Wasmuth J. A contig of non-chimaeric YACs containing the spinal muscular atrophy gene in 5q13. Hum Mol Genet. 1993 Aug;2(8):1161–1167. doi: 10.1093/hmg/2.8.1161. [DOI] [PubMed] [Google Scholar]
  16. Hahnen E., Forkert R., Marke C., Rudnik-Schöneborn S., Schönling J., Zerres K., Wirth B. Molecular analysis of candidate genes on chromosome 5q13 in autosomal recessive spinal muscular atrophy: evidence of homozygous deletions of the SMN gene in unaffected individuals. Hum Mol Genet. 1995 Oct;4(10):1927–1933. doi: 10.1093/hmg/4.10.1927. [DOI] [PubMed] [Google Scholar]
  17. Hahnen E., Schönling J., Rudnik-Schöneborn S., Raschke H., Zerres K., Wirth B. Missense mutations in exon 6 of the survival motor neuron gene in patients with spinal muscular atrophy (SMA). Hum Mol Genet. 1997 May;6(5):821–825. doi: 10.1093/hmg/6.5.821. [DOI] [PubMed] [Google Scholar]
  18. Kleyn P. W., Wang C. H., Lien L. L., Vitale E., Pan J., Ross B. M., Grunn A., Palmer D. A., Warburton D., Brzustowicz L. M. Construction of a yeast artificial chromosome contig spanning the spinal muscular atrophy disease gene region. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6801–6805. doi: 10.1073/pnas.90.14.6801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Laskey R. A., Mills A. D. Quantitative film detection of 3H and 14C in polyacrylamide gels by fluorography. Eur J Biochem. 1975 Aug 15;56(2):335–341. doi: 10.1111/j.1432-1033.1975.tb02238.x. [DOI] [PubMed] [Google Scholar]
  20. Lefebvre S., Bürglen L., Reboullet S., Clermont O., Burlet P., Viollet L., Benichou B., Cruaud C., Millasseau P., Zeviani M. Identification and characterization of a spinal muscular atrophy-determining gene. Cell. 1995 Jan 13;80(1):155–165. doi: 10.1016/0092-8674(95)90460-3. [DOI] [PubMed] [Google Scholar]
  21. Matthijs G., Schollen E., Legius E., Devriendt K., Goemans N., Kayserili H., Apäk M. Y., Cassiman J. J. Unusual molecular findings in autosomal recessive spinal muscular atrophy. J Med Genet. 1996 Jun;33(6):469–474. doi: 10.1136/jmg.33.6.469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Melki J., Abdelhak S., Sheth P., Bachelot M. F., Burlet P., Marcadet A., Aicardi J., Barois A., Carriere J. P., Fardeau M. Gene for chronic proximal spinal muscular atrophies maps to chromosome 5q. Nature. 1990 Apr 19;344(6268):767–768. doi: 10.1038/344767a0. [DOI] [PubMed] [Google Scholar]
  23. Melki J., Lefebvre S., Burglen L., Burlet P., Clermont O., Millasseau P., Reboullet S., Bénichou B., Zeviani M., Le Paslier D. De novo and inherited deletions of the 5q13 region in spinal muscular atrophies. Science. 1994 Jun 3;264(5164):1474–1477. doi: 10.1126/science.7910982. [DOI] [PubMed] [Google Scholar]
  24. Miller S. A., Dykes D. D., Polesky H. F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988 Feb 11;16(3):1215–1215. doi: 10.1093/nar/16.3.1215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Müller B., Melki J., Burlet P., Clerget-Darpoux F. Proximal spinal muscular atrophy (SMA) types II and III in the same sibship are not caused by different alleles at the SMA locus on 5q. Am J Hum Genet. 1992 May;50(5):892–895. [PMC free article] [PubMed] [Google Scholar]
  26. Parsons D. W., McAndrew P. E., Monani U. R., Mendell J. R., Burghes A. H., Prior T. W. An 11 base pair duplication in exon 6 of the SMN gene produces a type I spinal muscular atrophy (SMA) phenotype: further evidence for SMN as the primary SMA-determining gene. Hum Mol Genet. 1996 Nov;5(11):1727–1732. doi: 10.1093/hmg/5.11.1727. [DOI] [PubMed] [Google Scholar]
  27. Pearn J. Classification of spinal muscular atrophies. Lancet. 1980 Apr 26;1(8174):919–922. doi: 10.1016/s0140-6736(80)90847-8. [DOI] [PubMed] [Google Scholar]
  28. Rodrigues N. R., Owen N., Talbot K., Ignatius J., Dubowitz V., Davies K. E. Deletions in the survival motor neuron gene on 5q13 in autosomal recessive spinal muscular atrophy. Hum Mol Genet. 1995 Apr;4(4):631–634. doi: 10.1093/hmg/4.4.631. [DOI] [PubMed] [Google Scholar]
  29. Roy N., Mahadevan M. S., McLean M., Shutler G., Yaraghi Z., Farahani R., Baird S., Besner-Johnston A., Lefebvre C., Kang X. The gene for neuronal apoptosis inhibitory protein is partially deleted in individuals with spinal muscular atrophy. Cell. 1995 Jan 13;80(1):167–178. doi: 10.1016/0092-8674(95)90461-1. [DOI] [PubMed] [Google Scholar]
  30. Schwartz M., Sørensen N., Hansen F. J., Hertz J. M., Nørby S., Tranebjaerg L., Skovby F. Quantification, by solid-phase minisequencing, of the telomeric and centromeric copies of the survival motor neuron gene in families with spinal muscular atrophy. Hum Mol Genet. 1997 Jan;6(1):99–104. doi: 10.1093/hmg/6.1.99. [DOI] [PubMed] [Google Scholar]
  31. Sestini R., Orlando C., Zentilin L., Gelmini S., Pinzani P., Bianchi S., Selli C., Giacca M., Pazzagli M. Measuring c-erbB-2 oncogene amplification in fresh and paraffin-embedded tumors by competitive polymerase chain reaction. Clin Chem. 1994 Apr;40(4):630–636. [PubMed] [Google Scholar]
  32. Sestini R., Orlando C., Zentilin L., Lami D., Gelmini S., Pinzani P., Giacca M., Pazzagli M. Gene amplification for c-erbB-2, c-myc, epidermal growth factor receptor, int-2, and N-myc measured by quantitative PCR with a multiple competitor template. Clin Chem. 1995 Jun;41(6 Pt 1):826–832. [PubMed] [Google Scholar]
  33. Simard L. R., Vanasse M., Rochette C., Morgan K., Lemieux B., Melançon S. B., Labuda D. Linkage study of chronic childhood-onset spinal muscular atrophy (SMA): confirmation of close linkage to D5S39 in French Canadian families. Genomics. 1992 Sep;14(1):188–190. doi: 10.1016/s0888-7543(05)80305-2. [DOI] [PubMed] [Google Scholar]
  34. Talbot K., Ponting C. P., Theodosiou A. M., Rodrigues N. R., Surtees R., Mountford R., Davies K. E. Missense mutation clustering in the survival motor neuron gene: a role for a conserved tyrosine and glycine rich region of the protein in RNA metabolism? Hum Mol Genet. 1997 Mar;6(3):497–500. doi: 10.1093/hmg/6.3.497. [DOI] [PubMed] [Google Scholar]
  35. Thompson T. G., DiDonato C. J., Simard L. R., Ingraham S. E., Burghes A. H., Crawford T. O., Rochette C., Mendell J. R., Wasmuth J. J. A novel cDNA detects homozygous microdeletions in greater than 50% of type I spinal muscular atrophy patients. Nat Genet. 1995 Jan;9(1):56–62. doi: 10.1038/ng0195-56. [DOI] [PubMed] [Google Scholar]
  36. Velasco E., Valero C., Valero A., Moreno F., Hernández-Chico C. Molecular analysis of the SMN and NAIP genes in Spanish spinal muscular atrophy (SMA) families and correlation between number of copies of cBCD541 and SMA phenotype. Hum Mol Genet. 1996 Feb;5(2):257–263. doi: 10.1093/hmg/5.2.257. [DOI] [PubMed] [Google Scholar]
  37. Viollet L., Bertrandy S., Bueno Brunialti A. L., Lefebvre S., Burlet P., Clermont O., Cruaud C., Guénet J. L., Munnich A., Melki J. cDNA isolation, expression, and chromosomal localization of the mouse survival motor neuron gene (Smn). Genomics. 1997 Feb 15;40(1):185–188. doi: 10.1006/geno.1996.4551. [DOI] [PubMed] [Google Scholar]
  38. Wang C. H., Xu J., Carter T. A., Ross B. M., Dominski M. K., Bellcross C. A., Penchaszadeh G. K., Munsat T. L., Gilliam T. C. Characterization of survival motor neuron (SMNT) gene deletions in asymptomatic carriers of spinal muscular atrophy. Hum Mol Genet. 1996 Mar;5(3):359–365. doi: 10.1093/hmg/5.3.359. [DOI] [PubMed] [Google Scholar]
  39. Wirth B., Hahnen E., Morgan K., DiDonato C. J., Dadze A., Rudnik-Schöneborn S., Simard L. R., Zerres K., Burghes A. H. Allelic association and deletions in autosomal recessive proximal spinal muscular atrophy: association of marker genotype with disease severity and candidate cDNAs. Hum Mol Genet. 1995 Aug;4(8):1273–1284. doi: 10.1093/hmg/4.8.1273. [DOI] [PubMed] [Google Scholar]
  40. Wirth B., Pick E., Leutner A., Dadze A., Voosen B., Knapp M., Piechaczek-Wappenschmidt B., Rudnik-Schöneborn S., Schönling J., Cox S. Large linkage analysis in 100 families with autosomal recessive spinal muscular atrophy (SMA) and 11 CEPH families using 15 polymorphic loci in the region 5q11.2-q13.3. Genomics. 1994 Mar 1;20(1):84–93. doi: 10.1006/geno.1994.1130. [DOI] [PubMed] [Google Scholar]
  41. Wirth B., el-Agwany A., Baasner A., Burghes A., Koch A., Dadze A., Piechaczeck-Wappenschmidt B., Rudnik-Schöneborn S., Zerres K., Schönling J. Mapping of the spinal muscular atrophy (SMA) gene to a 750-kb interval flanked by two new microsatellites. Eur J Hum Genet. 1995;3(1):56–60. doi: 10.1159/000472274. [DOI] [PubMed] [Google Scholar]
  42. Zielenski J., Bozon D., Kerem B., Markiewicz D., Durie P., Rommens J. M., Tsui L. C. Identification of mutations in exons 1 through 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Genomics. 1991 May;10(1):229–235. doi: 10.1016/0888-7543(91)90504-8. [DOI] [PubMed] [Google Scholar]
  43. van der Steege G., Grootscholten P. M., Cobben J. M., Zappata S., Scheffer H., den Dunnen J. T., van Ommen G. J., Brahe C., Buys C. H. Apparent gene conversions involving the SMN gene in the region of the spinal muscular atrophy locus on chromosome 5. Am J Hum Genet. 1996 Oct;59(4):834–838. [PMC free article] [PubMed] [Google Scholar]
  44. van der Steege G., Grootscholten P. M., van der Vlies P., Draaijers T. G., Osinga J., Cobben J. M., Scheffer H., Buys C. H. PCR-based DNA test to confirm clinical diagnosis of autosomal recessive spinal muscular atrophy. Lancet. 1995 Apr 15;345(8955):985–986. [PubMed] [Google Scholar]

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