Validation of a high resolution NGS method for detecting spinal muscular atrophy carriers among phase 3 participants in the 1000 Genomes Project.

Jessica L Larson,Brett Spurrier,Dalin Chan,Lee M Silver,Ari J Silver,Carlos Borroto

doi:10.1186/s12881-015-0246-2

Jessica L Larson, Brett Spurrier + Show 4 more

Open Access

https://doi.org/10.1186/s12881-015-0246-2

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Abstract

BackgroundSpinal muscular atrophy (SMA) is the most common pan-ethnic cause of early childhood death due to mutations in a single gene, SMN1. Most chromosome 5 homologs have a functional gene and dysfunctional copy, SMN2, with a single synonymous base substitution that results in faulty RNA splicing. However, the copy number of SMN1 and SMN2 is highly variable, and one in 60 adults worldwide are SMA carriers. Although population-wide screening is recommended, current SMA carrier tests have not been incorporated into targeted gene panels.MethodsHere we describe a novel computational protocol for determining SMA carrier status based solely on individual exome data. Our method utilizes a Bayesian hierarchical model to quantify an individual’s carrier probability given only his or her SMN1 and SMN2 reads at six loci of interest.ResultsWe find complete concordance with results obtained with the current qPCR-based testing standard in known SMA carriers and affecteds. We applied our protocol to the phase 3 cohort of the 1,000 Genomes Project and found carrier frequencies in multiple populations consistent with the present literature.ConclusionOur process is a convenient, robust alternative to qPCR, which can easily be integrated into the analysis of large multi-gene NGS carrier screens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12881-015-0246-2) contains supplementary material, which is available to authorized users.

Highlights

Spinal muscular atrophy (SMA) is the most common pan-ethnic cause of early childhood death due to mutations in a single gene, SMN1
The volunteer samples were collected via saliva or semen; there was no difference in their average sequencing coverage (p-value = 0.195)
We analyzed six diagnosed nonSMA diseased control Coriell samples: two normal healthy controls (NHC), two with amyotrophic lateral sclerosis (ALS), one with Duchenne muscular dystrophy (DMD), and one with X-linked SMA (SMAX1). While four of these individuals are affected with a neuromuscular disease having a notable genetic component, they are only as likely as a randomly selected individual to be an SMA carrier

Summary

Introduction

Spinal muscular atrophy (SMA) is the most common pan-ethnic cause of early childhood death due to mutations in a single gene, SMN1. Spinal muscular atrophy (SMA) is a common autosomal recessive disorder affecting approximately 1/10,000 live births [1]. The disease results from the degeneration of spinal cord motor neurons, which leads to the progressive weakness and deterioration of skeletal muscle, and eventually paralysis and death [2]. Type I (OMIM: 253300) patients have severe muscle weakness within the first three months of life; All autosomal recessive forms of SMA disease are caused by variant forms of the SMN locus on chromosome 5 (chr5), which ordinarily contains two nearly identical copies of a gene encoding the survival of motor neuron gene product [4]. The two gene copies, referred to as SMN1 and SMN2, were derived through a recent duplication event along the human lineage (Fig. 1) [5].

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