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Considerations for clinical read alignment and mutational profiling using next-generation sequencing

Next-generation sequencing technologies are increasingly being applied in clinical settings, however the data are characterized by a range of platform-specific artifacts making downstream analysis problematic and error- prone. One major application of NGS is in the profiling of clinically relevant m...

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Detalles Bibliográficos
Autor principal: Oliver, Gavin R
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945748/
https://www.ncbi.nlm.nih.gov/pubmed/24627757
http://dx.doi.org/10.12688/f1000research.1-2.v2
Descripción
Sumario:Next-generation sequencing technologies are increasingly being applied in clinical settings, however the data are characterized by a range of platform-specific artifacts making downstream analysis problematic and error- prone. One major application of NGS is in the profiling of clinically relevant mutations whereby sequences are aligned to a reference genome and potential mutations assessed and scored. Accurate sequence alignment is pivotal in reliable assessment of potential mutations however selection of appropriate alignment tools is a non-trivial task complicated by the availability of multiple solutions each with its own performance characteristics. Using targeted analysis of BRCA1 as an example, we have simulated and mutated a test dataset based on Illumina sequencing technology. Our findings reveal key differences in the abilities of a range of common commercial and open source alignment tools to facilitate accurate downstream detection of a range of mutations. These observations will be of importance to anyone using NGS to profile mutations in clinical or basic research.