scholarly journals Population- and Variant-Based Genome Analyses of Viruses from Vaccine-Derived Rabies Cases Demonstrate Product Specific Clusters and Unique Patterns

Viruses ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 115
Author(s):  
Sten Calvelage ◽  
Marcin Smreczak ◽  
Anna Orłowska ◽  
Conrad Martin Freuling ◽  
Thomas Müller ◽  
...  
Keyword(s):  
Genetic Selection ◽  
Population Based ◽  
Vaccine Virus ◽  
Sequencing Data ◽  
Variant Analysis ◽  
Genome Analyses ◽  
Virus Strains ◽  
Generation Sequencing ◽  
Multiple Replication ◽  
Rabies Vaccination

Rabies in wildlife has been successfully controlled in parts of Europe and North America using oral rabies vaccination, i.e., the distribution of baits containing live-attenuated virus strains. Occasionally, these vaccines caused vaccine virus-induced rabies cases. To elucidate the mechanisms of genetic selection and the effect of viral populations on these rabies cases, a next generation sequencing approach as well as comprehensive data analyses of the genetic diversity of Street Alabama Dufferin (SAD) and ERA vaccine virus strains and vaccine-induced rabies cases from Canada and several European countries were conducted. As a result, twelve newly generated sets of sequencing data from Canada and Poland were added to a pool of previously investigated samples. While the population-based analysis showed a segregation of viruses of ERA vaccine-induced rabies cases from those of SAD Bern original (SAD Bernorig)-derived rabies cases, the in-depth variant analysis revealed three distinct combinations of selected variants for the ERA vaccine-induced cases, suggesting the presence of multiple replication-competent haplotypes in the investigated ERA-BHK21 vaccine. Our findings demonstrate the potential of a deep sequencing approach in combination with comprehensive analyses on the consensus, population, and variant level.

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 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 Manta: Rapid detection of structural variants and indels for clinical sequencing applications

2015 ◽  
Author(s):  
Xiaoyu Chen ◽  
Ole Schulz-Trieglaff ◽  
Richard Shaw ◽  
Bret Barnes ◽  
Felix Schlesinger ◽  
...  
Keyword(s):  
Clinical Analysis ◽  
Next Generation Sequencing Data ◽  
Normal Sample ◽  
Structural Variants ◽  
Sequencing Data ◽  
Community Resource ◽  
Split Read ◽  
Variant Analysis ◽  
Generation Sequencing ◽  
Better Than

Summary: We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid clinical analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50x genomic coverage is analyzed in less than 20 minutes. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to basepair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios. Availability: Manta source code and Linux binaries are available from http://github.com/Illumina/manta. Contact: [email protected]

scholarly journals An integrative variant analysis suite for whole exome next-generation sequencing data

2012 ◽  
Vol 13 (1) ◽  
pp. 8 ◽  
Author(s):  
Danny Challis ◽  
Jin Yu ◽  
Uday S Evani ◽  
Andrew R Jackson ◽  
Sameer Paithankar ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Whole Exome ◽  
Variant Analysis ◽  
Generation Sequencing
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