Artículo

Merino, G.A.; Murua, Y.A.; Fresno, C.; Sendoya, J.M.; Golubicki, M.; Iseas, S.; Coraglio, M.; Podhajcer, O.L.; Llera, A.S.; Fernández, E.A. "TarSeqQC: Quality control on targeted sequencing experiments in R" (2017) Human Mutation. 38(5):494-502
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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. © 2017 Wiley Periodicals, Inc.

Registro:

Documento: Artículo
Título:TarSeqQC: Quality control on targeted sequencing experiments in R
Autor:Merino, G.A.; Murua, Y.A.; Fresno, C.; Sendoya, J.M.; Golubicki, M.; Iseas, S.; Coraglio, M.; Podhajcer, O.L.; Llera, A.S.; Fernández, E.A.
Filiación: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
Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina
Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales, Buenos Aires, Argentina
Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina
Palabras clave:Cancer panel; experiment performance; medical genetics; quality control; R package; targeted sequencing
Año:2017
Volumen:38
Número:5
Página de inicio:494
Página de fin:502
DOI: http://dx.doi.org/10.1002/humu.23204
Título revista:Human Mutation
Título revista abreviado:Hum. Mutat.
ISSN:10597794
CODEN:HUMUE
Registro:http://digital.bl.fcen.uba.ar/collection/paper/document/paper_10597794_v38_n5_p494_Merino

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Citas:

---------- APA ----------
Merino, G.A., Murua, Y.A., Fresno, C., Sendoya, J.M., Golubicki, M., Iseas, S., Coraglio, M.,..., Fernández, E.A. (2017) . TarSeqQC: Quality control on targeted sequencing experiments in R. Human Mutation, 38(5), 494-502.
http://dx.doi.org/10.1002/humu.23204
---------- CHICAGO ----------
Merino, G.A., Murua, Y.A., Fresno, C., Sendoya, J.M., Golubicki, M., Iseas, S., et al. "TarSeqQC: Quality control on targeted sequencing experiments in R" . Human Mutation 38, no. 5 (2017) : 494-502.
http://dx.doi.org/10.1002/humu.23204
---------- MLA ----------
Merino, G.A., Murua, Y.A., Fresno, C., Sendoya, J.M., Golubicki, M., Iseas, S., et al. "TarSeqQC: Quality control on targeted sequencing experiments in R" . Human Mutation, vol. 38, no. 5, 2017, pp. 494-502.
http://dx.doi.org/10.1002/humu.23204
---------- VANCOUVER ----------
Merino, G.A., Murua, Y.A., Fresno, C., Sendoya, J.M., Golubicki, M., Iseas, S., et al. TarSeqQC: Quality control on targeted sequencing experiments in R. Hum. Mutat. 2017;38(5):494-502.
http://dx.doi.org/10.1002/humu.23204