ArticleHuman mutation2020
SMN1 copy-number and sequence variant analysis from next-generation sequencing data.
Article in Human mutation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- Characterisation of the SMN1/2 locus using a highly specific variant caller on whole-genome sequence data from 500,000 individuals.European journal of human genetics : EJHG · 2026Article
- Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.Bioinformatics (Oxford, England) · 2026Article
- MLDP-AS: an optimized next-generation sequencing assay for enhanced detection of technically challenging variants in expanded carrier screening.Journal of translational medicine · 2026Article
- Comprehensive analysis of NGS-based expanded carrier screening and follow-up in southern and southwestern China: results from 3024 Chinese individuals.Human genomics · 2024Article
- Diving into progress: a review on current therapeutic advancements in spinal muscular atrophy.Frontiers in neurology · 2024Review
- A multilocus approach for accurate variant calling in low-copy repeats using whole-genome sequencing.Bioinformatics (Oxford, England) · 2023Article
- Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing.American journal of human genetics · 2023Article
- Review
- Assessing clinical utility of preconception expanded carrier screening regarding residual risk for neurodevelopmental disorders.NPJ genomic medicine · 2022Article
- Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing.Nature communications · 2022Article
- Comprehensive analysis of recessive carrier status using exome and genome sequencing data in 1543 Southern Chinese.NPJ genomic medicine · 2022Article
- Next generation sequencing is a highly reliable method to analyze exon 7 deletion of survival motor neuron 1 (SMN1) gene.Scientific reports · 2022Article
- Genomic Variability in the Survival Motor Neuron Genes (International journal of molecular sciences · 2021Review
- SMN1 copy-number and sequence variant analysis from next-generation sequencing data.Human mutation · 2020Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.