insiM: in silico Mutator Software for Bioinformatics Pipeline Validation of Clinical Next-Generation Sequencing Assays.
J Mol Diagn
; 21(1): 19-26, 2019 01.
Article
em En
| MEDLINE
| ID: mdl-30273779
ABSTRACT
Lack of reliable reference samples containing different mutations of interest across large sets of disease-relevant loci limits the extensive validation clinical next-generation sequencing (NGS) assays and their associated bioinformatics pipelines. Herein, we have generated a publicly available, highly flexible tool, in silico Mutator (insiM), to introduce point mutations, insertions, deletions, and duplications of any size into real data sets of amplicon-based or hybrid-capture NGS assays. insiM accepts an alignment file along with target territory and produces paired-end FASTQ files containing specified mutations via modification of original sequencing reads. Mutant signal is, thus, generated within the context of existing real-world data to most closely mimic assay performance. Resulting files may then be passed through the assay's bioinformatics pipeline to assist with assay/bioinformatics validation and to identify performance gaps in detection. To establish the basic functionality of the software, a series of simulation experiments with varying mutation types, sizes, and allele frequencies were performed across the entire clinical territory of hybrid-capture and amplicon-based clinical assays developed at The University of Chicago. This work demonstrates the utility of insiM as a supplementary tool during the validation of an NGS assay's bioinformatics pipeline.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Sequenciamento de Nucleotídeos em Larga Escala
/
Mutação
Limite:
Animals
/
Humans
Idioma:
En
Revista:
J Mol Diagn
Assunto da revista:
BIOLOGIA MOLECULAR
Ano de publicação:
2019
Tipo de documento:
Article