New Approaches in Molecular Diagnosis and Population Carrier Screening for Spinal Muscular Atrophy

Abstract

Autosomal recessive spinal muscular atrophy, the leading genetic cause of infant death, is due to loss of functional SMN1 genes, mainly as a result of homozygous deletions. Carrier frequency in the general population varies widely from 1/50 to 1/125 and has significant counseling implications. In a cohort of 210 patients with spinal muscular atrophy confirmed at the molecular level, 91.9% had a homozygous deletion and 14 were compound heterozygotes. Two novel point mutations were detected (c.524delC and c.734dupC) and the 11 bp duplication c.770_780dup was found at a high frequency. We describe the development of a simple and robust method for homozygous deletion detection, which enabled us to simplify the diagnostic workup. Further, carrier frequency in our population was established by direct quantification with the commercially available MLPA kit, following optimization for the use of dried blood spots as sample specimens.

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References

Alías

, Bernal

, Fuentes-Prior

et al. 2009. Mutation update of spinal muscular atrophy in Spain: molecular characterization of 745 unrelated patients and identification of four novel mutations in the SMN1 gene. Hum Genet, 125:29-39.

Arkblad

, Darin

, Berg

et al. 2006. Multiplex ligation-dependent probe amplification improves diagnostics in spinal muscular atrophy. Neuromuscul Disord, 16:830-838.

Battaglia

, Princivalle

, Forti

et al. 1997. Expression of the SMN gene, the spinal muscular atrophy determining gene, in the mammalian central nervous system. Hum Mol Genet, 6:1961-1971.

Botta

, Tacconelli

, Bagni

et al. 2005. Transmission ratio distortion in the spinal muscular atrophy locus: data from 314 prenatal tests. Neurology, 65:1631-1635.

Brzustowicz

, Lehner

, Castilla

et al. 1990. Genetic mapping of chronic childhood-onset spinal muscular atrophy to chromosome 5q11.2-13.3. Nature, 344:540-541.

Burghes

AHM

. 1997. When is a deletion not a deletion? When it is converted. Am J Hum Genet, 61:9-15.

Cartegni

, Hastings

, Calarco

et al. 2006. Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. Am J Hum Genet, 78:63-77.

Cartegni

, Krainer

. 2002. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat Genet, 30:377-384.

Chen

, Wang

, Rennert

et al. 1999. Duplications and de novo deletions of the SMNt gene demonstrated by fluorescence-based carrier testing for spinal muscular atrophy. Am J Hum Genet, 85:463-469.

10.

Chen

, Dong

, Lin

et al. 2009. Rapid diagnosis of spinal muscular atrophy using high-resolution melting analysis. BMC Med Genet, 10:45.

11.

Clermont

, Burlet

, Benit

et al. 2004. Molecular analysis of SMA patients without homozygous SMN1 deletions using a new strategy for identification of SMN1 subtle mutations. Hum Mutat, 24:417-427.

12.

Coovert

, Le

, McAndrew

et al. 1997. The survival motor neuron protein in spinal muscular atrophy. Hum Mol Genet, 6:1205-1214.

13.

Cuscó

, Barceló

, del Río

et al. 2004. Detection of novel mutations in the SMN Tudor domain in type I SMA patients. Neurology, 63:146-149.

14.

Cusin

, Clermont

, Gerard

et al. 2003. Prevalence of SMN1 deletion and duplication in carrier and normal populations: implication for genetic counselling. J Med Genet, 40:E39.

15.

den Dunnen

, Antonarakis

. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat, 15:7-12.

16.

Eggermann

, Eggermann

, Elbracht

et al. 2009. A new splice site mutation in the SMN1 gene causes discrepant results in SMN1 deletion screening approaches. Neuromuscul Disord, 18:146-149.

17.

Gérard

, Ginet

, Matthijs

et al. 2000. Genotype determination at the survival motor neuron locus in a normal population and SMA carriers using competitive PCR and primer extension. Hum Mutat, 16:253-263.

18.

Hendrickson

, Donohoe

, Akmaev

et al. 2009. Differences in SMN1 allele frequencies among ethnic groups within North America. J Med Genet, 46:641-644.

19.

Kang

, Cho

, Chae

et al. 2009. False homozygous deletions of SMN1 exon 7 using Dra I PCR-RFLP caused by a novel mutation in spinal muscular atrophy. Genet Test Mol Biomarkers, 13:511-513.

20.

Kashima

, Manley

. 2003. A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy. Nat Genet, 34:460-463.

21.

Lacerda

, Amaral

, Pinto

et al. 1994. Gaucher disease: N370S glucocerebrosidase gene frequency in the Portuguese population. Clin Genet, 45:298-300.

22.

Lefebvre

, Burglen

, Reboullet

et al. 1995. Identification and characterization of a spinal muscular atrophy-determining gene. Cell, 80:155-165.

23.

Lunn

, Wang

. 2008. Spinal muscular atrophy. Lancet, 371:2120-2133.

24.

Martín

, Valero

, del Castillo

et al. 2002. Genetic study of SMA patients without homozygous SMN1 deletions: identification of compound heterozygotes and characterisation of novel intragenic SMN1 mutations. Hum Genet, 110:257-263.

25.

McAndrew

, Parsons

, Simard

et al. 1997. Identification of proximal spinal muscular atrophy carriers and patients by analysis of SMNT and SMNC gene copy number. Am J Hum Genet, 60:1411-1422.

26.

Meister

, Buhler

, Pillai

et al. 2001. A multiprotein complex mediates the ATP-dependent assembly of spliceosomal U snRNPs. Nat Cell Biol, 3:945-949.

27.

Melki

, Abdelhak

, Sheth

et al. 1990. Gene for chronic proximal spinal muscular atrophies maps to chromosome 5q. Nature, 344:767-778.

28.

Ogino

, Leonard

, Rennert

et al. 2001. Heteroduplex formation in SMN gene dosage analysis. J Mol Diagn, 3:150-157.

29.

Ogino

, Leonard

, Rennert

et al. 2002. Genetic risk assessment in carrier testing for spinal muscular atrophy. Am J Med Genet, 110:301-307.

30.

Ogino

, Wilson

, Gold

. 2004. New insights on the evolution of the SMN1 and SMN2 region: simulation and meta-analysis for allele and haplotype frequency calculations. Eur J Hum Genet, 12:1015-1023.

31.

Parsons

, McAndrew

, Allinson

et al. 1998. Diagnosis of spinal muscular atrophy in an SMN non-deletion patient using a quantitative PCR screen and mutation analysis. J Med Genet, 35:674-676.

32.

Parsons

, McAndrew

, Monani

et al. 1996. 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, 5:1727-1732.

33.

Pellizzoni

, Yong

, Dreyfuss

. 2002. Essential role for the SMN complex in the specificity of snRNP assembly. Science, 298:1775-1779.

34.

Pyatt

, Mihal

, Prior

. 2007. Assessment of liquid microbead arrays for the screening of newborns for spinal muscular atrophy. Clin Chem, 53:1879-1885.

35.

Scarciolla

, Stuppia

, De Angelis

et al. 2006. Spinal muscular atrophy genotyping by gene dosage using multiple ligation-dependent probe amplification. Neurogenetics, 7:269-276.

36.

Scheffer

, Cobben

, Matthijs

et al. 2001. Best practice guidelines for molecular analysis in spinal muscular atrophy. Eur J Hum Genet, 9:484-491.

37.

Setola

, Terao

, Locatelli

et al. 2007. Axonal-SMN (a-SMN), a protein isoform of the survival motor neuron gene, is specifically involved in axonogenesis. Proc Natl Acad Sci USA, 104:1959-1964.

38.

Simsek

, Al-Bulushi

, Shanmugakonar

et al. 2003. Allele-specific amplification of exon 7 in the survival motor neuron (SMN) genes for molecular diagnosis of spinal muscular atrophy. Genet Test, 7:325-327.

39.

Smith

, Calabro

, Chong

et al. 2007. Population screening and cascade testing for carriers of SMA. Eur J Hum Genet, 15:759-766.

40.

Sutomo

, Akutsu

, Takeshima

et al. 2002. Rapid SMN1 deletion test using DHPLC to screen patients with spinal muscular atrophy. Am J Med Genet, 113:225-226.

41.

Todd

, Shaw

, Morse

et al. 2010. SMN and the Gemin proteins form sub-complexes that localise to both stationary and dynamic neurite granules. Biochem Biophys Res Commun, 394:211-216.

42.

van der Steege

, Grootscholten

, van der Vlies

et al. 1995. PCR-based DNA test to confirm clinical diagnosis of autosomal recessive spinal muscular atrophy. Lancet, 345:985-986.

43.

Winkler

, Eggert

, Gradl

et al. 2005. Reduced U snRNP assembly causes motor axon degeneration in an animal model for spinal muscular atrophy. Genes Dev, 19:2320-2330.

44.

Wirth

, Herz

, Wetter

et al. 1999. Quantitative analysis of survival motor neuron copies: identification of subtle SMN1 mutations in patients with spinal muscular atrophy, genotype-phenotype correlation, and implications for genetic counseling. Am J Hum Genet, 64:1340-1356.

45.

Wirth

, Schmidt

, Hahnen

et al. 1997. De novo rearrangements found in 2% of index patients with spinal muscular atrophy: mutational mechanisms, parental origin, mutation rate, and implications for genetic counseling. Am J Hum Genet, 61:1102-1111.

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