Poster abstracts

Poster number 51 submitted by Corey Ruhno

Identification of Deletion Junctions and Variants that Affect Genotype-Phenotype Prediction in Spinal Muscular Atrophy

Corey Ruhno (Department of Biochemistry and Chemical Pharmacology, The Ohio State University, Columbus OH), Vicki McGovern (Department of Biochemistry and Chemical Pharmacology, The Ohio State University, Columbus OH), Matthew Avenarius, Pamela J. Snyder, Thomas W. Prior (Department of Pathology, The Ohio State University, Columbus OH), Flavia Nery, Kathryn Swoboda ( Department of Neurology, MassGeneral Hospital for Children, Boston MA), Jennifer Rogenbuck, John T. Kissel (Department of Neurology, The Ohio State University, Columbus OH), Arthur H.M. Burghes (Department of Biochemistry and Chemical Pharmacology, The Ohio State University, Columbus OH)

Abstract:
Spinal muscular atrophy is a degenerative motor neuron disease that is caused by low levels of the SMN protein. SMA severity is inversely correlated with SMN2 copy number, however exceptions to this are not uncommon. The region of the genome that contains SMN1 and SMN2 is very unstable and contains numerous repeats, making it prone to genomic rearrangements like inversions and deletions. Mismatches between the copy number of SMN2 when measured at the 5' marker AG1-CA and exon 7 indicate possible partial deletions of SMN2. Despite this, no deletion breakpoints have been determined in the region. We have sequenced the SMN2 genes of nearly 200 patients and developed a bioinformatic pipeline for identifying deletions, inversions, and variants that could modify SMN2 and thus the SMA phenotype. We have identified two different deletions, both of which result in loss of exons 7 and 8, rendering the gene non-functional. We have screened for the prevalence of one of these deletions amongst populations of individuals with varying copy number of SMN1 and SMN2. It was most prevalent in individuals with 0 copies of SMN2 and 1 copy of SMN1, with a prevalence of 63%. Other genotypes with a high prevalence of the deletion include 2 SMN1/0 SMN2 at 46%, 0 SMN1/1 SMN2 at 35%, and 2 SMN1/1 SMN2 at 34%. While this deletion is more common in SMN2 it clearly does occur in SMN1. We also have identified exonic variants that lie in the SMN2 gene that alter SMN2 function. PLS3 was also captured but no association was found between milder than expected patients and variants known to increase PLS3 expression. In order to identify variants outside of SMN2 that alter severity of SMA we have performed whole genome sequencing of 3 families with discordant sibling phenotypes and 4 with concordant phenotypes as controls. We have found 23 exonic variants that segregate with the milder than expected phenotypes and many intronic variants as well. We are also performing pathway analysis with this data set to identify the critical genes. Candidate genes/pathways that are expressed in motor neurons are tested in additional families.

References:
Pearn J. Incidence, prevalence, and gene frequency studies of chronic childhood spinal muscular atrophy. J Med Genet. 1978;15:409-413. doi:10.1136/jmg.15.6.409.
McAndrew PE, Parsons DW, Simard LR, Rochette C, Ray PN, Mendell JR, Prior TW, Burghes a H. Identification of proximal spinal muscular atrophy carriers and patients by analysis of SMNT and SMNC gene copy number. Am J Hum Genet. 1997;60(6):1411-22. doi:10.1086/515465.
Coovert DD, Le TT, Mcandrew PE, Strasswimmer J, Crawford TO, Mendell JR, Coulson SE, Androphy EJ, Prior TW, Burghes AHM. The survival motor neuron protein in spinal muscular atrophy. 1997;6(8):21-22.
Lefebvre S, Burlet P, Liu Q. Correlation between severity and SMN protein level in spinal muscular atrophy. Nat Genet. 1997;16.

Keywords: spinal muscular atrophy, modifier, bioinformatics