title: TarSeqQC: Quality control on targeted sequencing experiments in R.
abstract: Targeted sequencing (TS) is growing as a screening methodology used in research and medical genetics to identify genomic alterations causing human diseases. In general, a list of possible genomic variants is derived from mapped reads through a variant calling step. This processing step is usually based on variant coverage, although it may be affected by several factors. Therefore, undercovered relevant clinical variants may not be reported, affecting pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and to avoid erroneous medical conclusions. There are several quality control tools, but they are focused on issues related to whole-genome sequencing. However, in TS, quality control should assess experiment, gene, and genomic region performances based on achieved coverages. Here, we propose TarSeqQC R package for quality control in TS experiments. The tool is freely available at Bioconductor repository. TarSeqQC was used to analyze two datasets; low-performance primer pools and features were detected, enhancing the quality of experiment results. Read count profiles were also explored, showing TarSeqQC's effectiveness as an exploration tool. Our proposal may be a valuable bioinformatic tool for routinely TS experiments in both research and medical genetics.
authors.affiliation: Ua Area Cs. Agr. Ing. Bio. Y S, Conicet, Universidad Católica de Córdoba, Córdoba, Argentina.|Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina.
authors.forename: Gabriela A
authors.initials: GA
authors.lastname: Merino
authors.affiliation: Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina.
authors.forename: Yanina A
authors.initials: YA
authors.lastname: Murua
authors.affiliation: Ua Area Cs. Agr. Ing. Bio. Y S, Conicet, Universidad Católica de Córdoba, Córdoba, Argentina.
authors.forename: Cristóbal
authors.initials: C
authors.lastname: Fresno
authors.affiliation: Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina.
authors.forename: Juan M
authors.initials: JM
authors.lastname: Sendoya
authors.affiliation: Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales, Buenos Aires, Argentina.
authors.forename: Mariano
authors.initials: M
authors.lastname: Golubicki
authors.affiliation: Hospital de Gastroenterología "Dr. Carlos Bonorino Udaondo", Buenos Aires, Argentina.
authors.forename: Soledad
authors.initials: S
authors.lastname: Iseas
authors.affiliation: Hospital de Gastroenterología "Dr. Carlos Bonorino Udaondo", Buenos Aires, Argentina.
authors.forename: Mariana
authors.initials: M
authors.lastname: Coraglio
authors.affiliation: Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina.
authors.forename: Osvaldo L
authors.initials: OL
authors.lastname: Podhajcer
authors.affiliation: Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina.
authors.forename: Andrea S
authors.initials: AS
authors.lastname: Llera
authors.affiliation: Ua Area Cs. Agr. Ing. Bio. Y S, Conicet, Universidad Católica de Córdoba, Córdoba, Argentina.|Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina.
authors.forename: Elmer A
authors.initials: EA
authors.lastname: Fernández
mesh_terms: D019295:Computational Biology / Q000379:methods* / Q000592:standards; D066264:Datasets as Topic; D023281:Genomics / Q000379:methods* / Q000592:standards; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D011786:Quality Control; D015203:Reproducibility of Results; D012984:Software / Q000592:standards; D014584:User-Computer Interface
keywords: Cancer panel; R package; experiment performance; medical genetics; quality control; targeted sequencing