scholarly journals SMN1 copy‐number and sequence variant analysis from next‐generation sequencing data

2020 ◽  
Vol 41 (12) ◽  
pp. 2073-2077
Author(s):  
Daniel Lopez‐Lopez ◽  
Carlos Loucera ◽  
Rosario Carmona ◽  
Virginia Aquino ◽  
Josefa Salgado ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Next Generation Sequencing Data ◽  
Sequence Variant ◽  
Next Generation ◽  
Sequencing Data ◽  
Variant Analysis ◽  
Generation Sequencing

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

2020 ◽  
Author(s):  
Daniel Lopez-Lopez ◽  
Carlos Loucera ◽  
Rosario Carmona ◽  
Virginia Aquino ◽  
Josefa Salgado ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Muscular Atrophy ◽  
Sequence Similarity ◽  
Homozygous Deletion ◽  
Next Generation Sequencing Data ◽  
Sequence Variant ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

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 on Github at: www.github.com/babelomics/SMAca

A Benchmark of Structural Variant Analysis Tools for Next Generation Sequencing Data

2013 ◽  
Vol 2 (4) ◽  
pp. 86-98
Author(s):  
Chatzinikolaou Panagiotis ◽  
Makris Christos ◽  
Dimitrios Vlachakis ◽  
Sophia Kossida
Keyword(s):  
Next Generation Sequencing ◽  
Level Structure ◽  
Atomic Level ◽  
Protein Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Variant Analysis ◽  
Generation Sequencing

In language of genetics and biochemistry, sequencing is the determination of an unbranched biopolymer's primary structure. A sequence is a symbolic linear depiction, result of sequencing. This sequence is a succinct summary of the most of the sequenced molecule's atomic-level structure. (Most known is DNA-sequencing, RNA-sequencing, Protein-sequencing and Next-Generation-sequencing)

scholarly journals cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

2012 ◽  
Vol 40 (9) ◽  
pp. e69-e69 ◽  
Author(s):  
Günter Klambauer ◽  
Karin Schwarzbauer ◽  
Andreas Mayr ◽  
Djork-Arné Clevert ◽  
Andreas Mitterecker ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
False Discovery Rate ◽  
Copy Number ◽  
Copy Number Variations ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
False Discovery ◽  
Generation Sequencing

scholarly journals Assessing Copy Number Alterations in Targeted, Amplicon-Based Next-Generation Sequencing Data

2015 ◽  
Vol 17 (1) ◽  
pp. 53-63 ◽  
Author(s):  
Catherine Grasso ◽  
Timothy Butler ◽  
Katherine Rhodes ◽  
Michael Quist ◽  
Tanaya L. Neff ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Next Generation Sequencing Data ◽  
Copy Number Alterations ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

2011 ◽  
Vol 28 (3) ◽  
pp. 423-425 ◽  
Author(s):  
Valentina Boeva ◽  
Tatiana Popova ◽  
Kevin Bleakley ◽  
Pierre Chiche ◽  
Julie Cappo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing
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