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

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

Content Provider	Europe PMC
Author	Lopez‐Lopez, Daniel Loucera, Carlos Carmona, Rosario Aquino, Virginia Salgado, Josefa Pasalodos, Sara Miranda, María Alonso, Ángel Dopazo, Joaquín
Abstract	AbstractSpinal 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.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7756735&blobtype=pdf
Page Count	5
ISSN	10597794
Journal	Human Mutation [Hum Mutat]
Volume Number	41
DOI	10.1002/humu.24120
PubMed Central reference number	PMC7756735
Issue Number	12
PubMed reference number	33058415
e-ISSN	10981004
Language	English
Publisher	John Wiley and Sons Inc.
Publisher Date	2020-10-14
Publisher Place	Hoboken
Access Restriction	Open
Rights License	This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2020 The Authors. Human Mutation Published by Wiley Periodicals LLC
Subject Keyword	next generation sequencing pipeline SMA
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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