Molecular analysis of spinal muscular atrophy and modification of the phenotype by SMN2

Abstract

Purpose: This study describes SMN1 deletion frequency, carrier studies, and the effect of the modifying SMN2 gene on the spinal muscular atrophy (SMA) phenotype. A novel allele-specific intragenic mutation panel increases the sensitivity of SMN1 testing. Methods: From 1995 to 2001, 610 patients were tested for SMN1 deletions and 399 relatives of probands have been tested for carrier status. SMN2 copy number was compared between 52 type I and 90 type III patients, and between type I and type III patients with chimeric SMN genes. A fluorescent allele-specific polymerase chain reaction (PCR) -based strategy detected intragenic mutations in potential compound heterozygotes and was used on 366 patients. Results: Less than half of the patients tested were homozygously deleted for SMN1. A PCR-based panel detected the seven most common intragenic mutations. SMN2 copy number was significantly different between mild and severely affected patients. Conclusions: SMN1 molecular testing is essential for the diagnosis of SMA and allows for accurate carrier testing.Screening for intragenic mutations in SMN1 increases the sensitivity of diagnostic testing. Finally, SMN2 copy number is conclusively shown to ameliorate the phenotype and provide valuable prognostic information. Genet Key Words: spinal muscular atrophy, SMN, polymerase chain reactionSpinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease caused by homozygous mutation of the SMN1 gene 1 on chromosome 5q13. 2-12 5q-SMA has an incidence of 1/10,000 with an estimated carrier frequency of 1/50. [13][14][15][16][17] Deletion and gene conversion events result in a 95% to 98% rate of homozygous loss of the SMN1 gene in patients with classic SMA. 1,18 -31 A further 1% to 3% of well-characterized SMA cases are the result of compound heterozygosity with an intragenic mutation and a deletion. 31,32 Clinically, SMA patients are classified as type I, II, or III, based on the severity of the disease and the age of onset. 33,34 SMA type I, also known as Werdnig-Hoffmann disease, 35,36 is the most severe presentation. Type I infants are hypotonic and have severe proximal muscle wasting due to a lack of ␣-motor neurons in the anterior horn of the spinal cord. These patients are diagnosed prenatally or within 6 months after birth. They never sit unaided and usually die within the first 2 years, most often due to respiratory muscle weakness. Patients with intermediate SMA type II develop the disease before 18 months of age. They are able to sit unaided, but do not stand or walk. SMA type III, also called Kugelberg-Welander disease, is less severe. 37,38 Type III patients are diagnosed after 18 months, are able to walk, can have children, and often live at least into the second or third decade. 39 This study presents the clinical experience of 6 years of SMA testing in the Molecular Pathology Laboratory at The Ohio State University. Despite the fact that more than 95% of 5q-linked SMA patients lack any intact SMN1, it has been our experience that Ͻ43% of patients ...

Parental attitudes toward newborn screening for Duchenne/Becker muscular dystrophy and spinal muscular atrophy

“…People with SMA must have at least 1 copy of SMN2, but there is still variability. 1-2 copies of SMN2 is most often associated with SMA type I; people with SMA type II typically have 3 copies; and the majority of people with SMA type III have 3-4 copies (Gerard, 2000;Mailman, 2002;Prior, 2010). This variability and overlap of SMN2 copy number between clinical presentations makes it difficult to predict prognosis based on SMN2 copy number alone (Wang, 2007).…”

New insights on the evolution of the SMN1 and SMN2 region: simulation and meta-analysis for allele and haplotype frequency calculations

“…Likewise, to calculate e, f, and g, we used population data based on large numbers of SMA patients (ie, formulae (7) through (10)), rather than small numbers of carrier individuals (ie, formulae (11) through (15)). The potential existence of a haplotype with three copies of SMN1 might compromise the accuracy of estimates based primarily on formulae (25) through (27), and, to lesser degrees, on formulae (21) through (24). Thus, we did not primarily use formulae (25) through (27).…”

Spinal muscular atrophy – novel therapies, new challenges

“…Pacjenci z formą ostrą mają zwykle 1 do 2 kopii, z postacią pośrednią od 2 do 3, a z formą łagodną 3-4 a nawet 5 i 6 kopii. [25][26][27] Wpływ liczby kopii genu SMN2 nie tłuma-czy jednak całkowicie zmienności fenotypowej (np. 3 kopie SMN2 obserwuje się zarówno w SMA1 jak i SMA3).…”