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SMN1 copy-number and sequence variant analysis from next-generation sequencing data.

ABSTRACT: Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next-generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available at https://www.github.com/babelomics/SMAca.

SUBMITTER: Lopez-Lopez D 

PROVIDER: S-EPMC7756735 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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SMN1 copy-number and sequence variant analysis from next-generation sequencing data.

Lopez-Lopez Daniel D   Loucera Carlos C   Carmona Rosario R   Aquino Virginia V   Salgado Josefa J   Pasalodos Sara S   Miranda María M   Alonso Ángel Á   Dopazo Joaquín J  

Human mutation 20201014 12

Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next-generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and es  ...[more]

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