TarSeqQC: Quality control on targeted sequencing experiments in R
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 ba...
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| Otros Autores: | , , , , , , , , |
| Formato: | Capítulo de libro |
| Lenguaje: | Inglés |
| Publicado: |
John Wiley and Sons Inc.
2017
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| Acceso en línea: | Registro en Scopus DOI Handle Registro en la Biblioteca Digital |
| Aporte de: | Registro referencial: Solicitar el recurso aquí |
| LEADER | 08869caa a22008297a 4500 | ||
|---|---|---|---|
| 001 | PAPER-15041 | ||
| 003 | AR-BaUEN | ||
| 005 | 20230518204540.0 | ||
| 008 | 170725s2017 xx ||||fo|||| 00| 0 eng|d | ||
| 024 | 7 | |2 scopus |a 2-s2.0-85017340504 | |
| 040 | |a Scopus |b spa |c AR-BaUEN |d AR-BaUEN | ||
| 030 | |a HUMUE | ||
| 100 | 1 | |a Merino, G.A. | |
| 245 | 1 | 0 | |a TarSeqQC: Quality control on targeted sequencing experiments in R |
| 260 | |b John Wiley and Sons Inc. |c 2017 | ||
| 270 | 1 | 0 | |m Merino, G.A.; Ua Area Cs. Agr. Ing. Bio. Y S, Conicet, Universidad Católica de CórdobaArgentina; email: gmerino@bdmg.com.ar |
| 506 | |2 openaire |e Política editorial | ||
| 504 | |a 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 | ||
| 504 | |a Comprehensive molecular characterization of human colon and rectal cancer (2012) Nature, 487, pp. 330-337 | ||
| 504 | |a Chang, F., Li, M.M., Clinical application of amplicon-based next-generation sequencing in cancer (2013) Cancer Genetics, 206, pp. 413-419 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform (2009) Bioinformatics, 25, pp. 1754-1760 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a Metzker, M.L., Sequencing technologies—The next generation (2010) Nature Reviews Genetics, 11, pp. 31-46 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a 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 | ||
| 504 | |a Rizzo, J.M., Buck, M.J., Key principles and clinical applications of “next-generation” DNA sequencing (2012) Cancer Prevention Research, 5, pp. 887-900 | ||
| 504 | |a Satya, R.V., Di Carlo, J., Edge effects in calling variants from targeted amplicon sequencing (2014) BMC Genomics, 15, p. 1073 | ||
| 504 | |a 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 | ||
| 504 | |a Segditsas, S., Tomlinson, I., Colorectal cancer and genetic alterations in the Wnt pathway (2006) Oncogene, 25, pp. 7531-7537 | ||
| 504 | |a 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 | ||
| 520 | 3 | |a 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. |l eng | |
| 536 | |a Detalles de la financiación: BOD/2016, UCC, Universidad Católica de Córdoba | ||
| 536 | |a Detalles de la financiación: PBIT 015/13, MINCyT, Ministerio de Ciencia, Tecnología e Innovación Productiva | ||
| 536 | |a Detalles de la financiación: PPL04/2011, FonCyT, Fondo para la Investigación Científica y Tecnológica | ||
| 536 | |a Detalles de la financiación: PPL06/2011, FonCyT, Fondo para la Investigación Científica y Tecnológica | ||
| 593 | |a Ua Area Cs. Agr. Ing. Bio. Y S, Conicet, Universidad Católica de Córdoba, Córdoba, Argentina | ||
| 593 | |a Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina | ||
| 593 | |a Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina | ||
| 593 | |a Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales, Buenos Aires, Argentina | ||
| 593 | |a Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”, Buenos Aires, Argentina | ||
| 690 | 1 | 0 | |a CANCER PANEL |
| 690 | 1 | 0 | |a EXPERIMENT PERFORMANCE |
| 690 | 1 | 0 | |a MEDICAL GENETICS |
| 690 | 1 | 0 | |a QUALITY CONTROL |
| 690 | 1 | 0 | |a R PACKAGE |
| 690 | 1 | 0 | |a TARGETED SEQUENCING |
| 700 | 1 | |a Murua, Y.A. | |
| 700 | 1 | |a Fresno, C. | |
| 700 | 1 | |a Sendoya, J.M. | |
| 700 | 1 | |a Golubicki, M. | |
| 700 | 1 | |a Iseas, S. | |
| 700 | 1 | |a Coraglio, M. | |
| 700 | 1 | |a Podhajcer, O.L. | |
| 700 | 1 | |a Llera, A.S. | |
| 700 | 1 | |a Fernández, E.A. | |
| 773 | 0 | |d John Wiley and Sons Inc., 2017 |g v. 38 |h pp. 494-502 |k n. 5 |x 10597794 |t Hum. Mutat. | |
| 856 | 4 | 1 | |u https://www.scopus.com/inward/record.uri?eid=2-s2.0-85017340504&doi=10.1002%2fhumu.23204&partnerID=40&md5=752e32cfc925d9264ab7706a533b26c7 |y Registro en Scopus |
| 856 | 4 | 0 | |u https://doi.org/10.1002/humu.23204 |y DOI |
| 856 | 4 | 0 | |u https://hdl.handle.net/20.500.12110/paper_10597794_v38_n5_p494_Merino |y Handle |
| 856 | 4 | 0 | |u https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10597794_v38_n5_p494_Merino |y Registro en la Biblioteca Digital |
| 961 | |a paper_10597794_v38_n5_p494_Merino |b paper |c PE | ||
| 962 | |a info:eu-repo/semantics/article |a info:ar-repo/semantics/artículo |b info:eu-repo/semantics/publishedVersion | ||
| 999 | |c 75994 | ||