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
Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

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:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10597794_v38_n5_p494_Merino

Referencias:

  • Becker, K., Vollbrecht, C., Koitzsch, U., Koenig, K., Fassunke, J., Huss, S., Merkelbach-Bruse, S., Deep ion sequencing of amplicon adapter ligated libraries: A novel tool in molecular diagnostics of formalin fixed and paraffin embedded tissues (2013) Journal of Clinical Pathology, 66, pp. 803-806
  • Comprehensive molecular characterization of human colon and rectal cancer (2012) Nature, 487, pp. 330-337
  • Chang, F., Li, M.M., Clinical application of amplicon-based next-generation sequencing in cancer (2013) Cancer Genetics, 206, pp. 413-419
  • Hadd, A.G., Houghton, J., Choudhary, A., Sah, S., Chen, L., Marko, A.C., Latham, G.J., Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens (2013) The Journal of Molecular Diagnostics, 15, pp. 234-247
  • Harismendy, O., Schwab, R.B., Alakus, H., Yost, S.E., Matsui, H., Hasteh, F., Frazer, K.A., Evaluation of ultra-deep targeted sequencing for personalized breast cancer care (2013) Breast Cancer Research, 15, p. 115
  • Hummel, M., Bonnin, S., Lowy, E., Roma, G., TEQC: An R package for quality control in target capture experiments (2011) Bioinformatics, 27, pp. 1316-1317
  • Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform (2009) Bioinformatics, 25, pp. 1754-1760
  • Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., The Sequence Alignment/Map (SAM) format and SAMtools (2009) Bioinformatics, 25, pp. 2078-2079
  • Martínez-Alcántara, A., Ballesteros, E., Feng, C., Rojas, M., Koshinsky, H., Fofanov, V.Y., Fofanov, Y., PIQA: Pipeline for Illumina G1 genome analyzer data quality assessment (2009) Bioinformatics, 25, pp. 2438-2439
  • Meldrum, C., Doyle, M.A., Tothill, R.W., Next-generation sequencing for cancer diagnostics: A practical perspective (2011) The Clinical Biochemist Reviews, 32, pp. 177-195
  • Merino, G.A., Fresno, C., Koile, D., Yankilevich, P., Sendoya, J.M., Oliver, J., Fernández, E.A., An exploration tool for quality analysis in targeted sequencing experiments (2015) IFMBE Proceedings, 49, pp. 659-662
  • Metzker, M.L., Sequencing technologies—The next generation (2010) Nature Reviews Genetics, 11, pp. 31-46
  • Morgan, M., Anders, S., Lawrence, M., Aboyoun, P., Pages, H., Gentleman, R., ShortRead: A bioconductor package for input, quality assessment and exploration of high-throughput sequence data (2009) Bioinformatics, 25, pp. 2607-2608
  • Mouradov, D., Sloggett, C., Jorissen, R.N., Love, C.G., Li, S., Burgess, A.W., Sieber, O.M., Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer (2014) Cancer Research, 74, pp. 3238-3247
  • Nielsen, R., Paul, J.S., Albrechtsen, A., Song, Y.S., Genotype and SNP calling from next-generation sequencing data (2011) Nature Reviews Genetics, 126, pp. 443-451
  • Nieuwenhuis, M.H., Vasen, H.F.A., Correlations between mutation site in APC and phenotype of familial adenomatous polyposis (FAP): A review of the literature (2007) Critical Reviews in Oncology/Hematology, 61, pp. 153-161
  • Nikiforova, M.N., Wald, A.I., Roy, S., Durso, M.B., Nikiforov, Y.E., Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer (2013) The sJournal of Clinical Endocrinology & Metabolism, 98, pp. E1852-E1860
  • Rizzo, J.M., Buck, M.J., Key principles and clinical applications of “next-generation” DNA sequencing (2012) Cancer Prevention Research, 5, pp. 887-900
  • Satya, R.V., Di Carlo, J., Edge effects in calling variants from targeted amplicon sequencing (2014) BMC Genomics, 15, p. 1073
  • Schweiger, M.R., Kerick, M., Timmermann, B., Isau, M., The power of NGS technologies to delineate the genome organization in cancer: From mutations to structural variations and epigenetic alterations (2011) Cancer and Metastasis Reviews, 30, pp. 199-210
  • Segditsas, S., Tomlinson, I., Colorectal cancer and genetic alterations in the Wnt pathway (2006) Oncogene, 25, pp. 7531-7537
  • Yost, S.E., Alakus, H., Matsui, H., Schwab, R.B., Jepsen, K., Frazer, K.A., Harismendy, O., Mutascope: Sensitive detection of somatic mutations from deep amplicon sequencing (2013) Bioinformatics, 29, pp. 1908-1909

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