CIDIE   24052
CENTRO DE INVESTIGACION Y DESARROLLO EN INMUNOLOGIA Y ENFERMEDADES INFECCIOSAS
Unidad Ejecutora - UE
artículos
Título:
TarSeqQC: Quality control on targeted sequencing experiments in R
Autor/es:
FRESNO, CRISTÓBAL; ISEAS, SOLEDAD; LLERA, ANDREA S.; MURUA, YANINA A.; GOLUBICKI, MARIANO; PODHAJCER, OSVALDO L.; MERINO, GABRIELA A.; SENDOYA, JUAN M.; CORAGLIO, MARIANA; FERNÁNDEZ, ELMER A.; FRESNO, CRISTÓBAL; ISEAS, SOLEDAD; LLERA, ANDREA S.; MURUA, YANINA A.; GOLUBICKI, MARIANO; PODHAJCER, OSVALDO L.; MERINO, GABRIELA A.; SENDOYA, JUAN M.; CORAGLIO, MARIANA; FERNÁNDEZ, ELMER A.
Revista:
HUMAN MUTATION
Editorial:
WILEY-LISS, DIV JOHN WILEY & SONS INC
Referencias:
Lugar: New York; Año: 2017 vol. 38 p. 494 - 502
ISSN:
1059-7794
Resumen:
Targeted sequencing is growing as a screening methodology used in research and medical geneticsto identify genomic alterations causing human diseases. In general, a list of possible genomicvariants is derived from mapped reads through a variant calling step. This processing step is usuallybased on variant coverage, although it may be affected by several factors. Therefore, under-coveredrelevant clinical variants may not be reported, impacting on pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and toavoid erroneous medical conclusions. There are several quality control tools, but they are focused onissues related to whole genome sequencing. However, in targeted sequencing, quality control shouldassess experiment, gene and genomic region performances based on achieved coverages.Here, we propose TarSeqQC R package for quality control in targeted sequencing experiments. Thetool 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 experimentresults. Read count profiles were also explored, showing TarSeqQC?s effectiveness as an explorationtool. Our proposal may be a valuable bioinformatic tool for routinely targeted sequencingexperiments in both research and medical genetics.