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Showing 1 to 5 of 5 entries
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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing.

Journal of visualized experiments : JoVE

Lv X, Zhao M, Yi Y, Zhang L, Guan Y, Liu T, Yang L, Chen R, Ma J, Yi X.
PMID: 28872127
J Vis Exp. 2017 Aug 24;(126). doi: 10.3791/56342.

The analysis of circulating tumor DNA (ctDNA) using next-generation sequencing (NGS) has become a valuable tool for the development of clinical oncology. However, the application of this method is challenging due to its low sensitivity in analyzing the trace...

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Lv X, Zhao M, Yi Y, et al. Detection of Rare Mutations in CtDNA Using Next Generation Sequencing. J Vis Exp. 2017;(126)doi: 10.3791/56342.
Lv, X., Zhao, M., Yi, Y., Zhang, L., Guan, Y., Liu, T., Yang, L., Chen, R., Ma, J., & Yi, X. (2017). Detection of Rare Mutations in CtDNA Using Next Generation Sequencing. Journal of visualized experiments : JoVE, (126), . https://doi.org/10.3791/56342
Lv, Xiaoxing, et al. "Detection of Rare Mutations in CtDNA Using Next Generation Sequencing." Journal of visualized experiments : JoVE vol. ,126 (2017). doi: https://doi.org/10.3791/56342
Lv X, Zhao M, Yi Y, Zhang L, Guan Y, Liu T, Yang L, Chen R, Ma J, Yi X. Detection of Rare Mutations in CtDNA Using Next Generation Sequencing. J Vis Exp. 2017 Aug 24;(126). doi: 10.3791/56342. PMID: 28872127; PMCID: PMC5614374.
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[Molecular research methods in the detection of germinal mutations in hereditary colorectal cancer].

Revista de gastroenterologia del Peru : organo oficial de la Sociedad de Gastroenterologia del Peru

Dominguez MV, Bastos EP, Silva SD, Rossi BM.
PMID: 19898597
Rev Gastroenterol Peru. 2009 Jul-Sep;29(3):247-53.

Colorectal cancer (CRC) is one of the main causes of death in South American countries. The hereditary forms of CRC are, familial adenomatous (FAP) and hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch Syndrome (LS), which is the most common...

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Dominguez MV, Bastos EP, Silva SD, et al. Metodos de investigacion molecular en la deteccion de mutaciones germinativas en cancer colorrectal hereditario. [Molecular research methods in the detection of germinal mutations in hereditary colorectal cancer]. Rev Gastroenterol Peru. 2009;29(3):247-53
Dominguez, M. V., Bastos, E. P., Silva, S. D., & Rossi, B. M. (2009). Metodos de investigacion molecular en la deteccion de mutaciones germinativas en cancer colorrectal hereditario. [Molecular research methods in the detection of germinal mutations in hereditary colorectal cancer]. Revista de gastroenterologia del Peru : organo oficial de la Sociedad de Gastroenterologia del Peru, 29(3), 247-53.
Dominguez, M V, et al. "Metodos de investigacion molecular en la deteccion de mutaciones germinativas en cancer colorrectal hereditario." [Molecular research methods in the detection of germinal mutations in hereditary colorectal cancer]. Revista de gastroenterologia del Peru : organo oficial de la Sociedad de Gastroenterologia del Peru vol. 29,3 (2009): 247-53.
Dominguez MV, Bastos EP, Silva SD, Rossi BM. Metodos de investigacion molecular en la deteccion de mutaciones germinativas en cancer colorrectal hereditario. [Molecular research methods in the detection of germinal mutations in hereditary colorectal cancer]. Rev Gastroenterol Peru. 2009 Jul-Sep;29(3):247-53. Spanish. PMID: 19898597.
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GAMES identifies and annotates mutations in next-generation sequencing projects.

Bioinformatics (Oxford, England)

Sana ME, Iascone M, Marchetti D, Palatini J, Galasso M, Volinia S.
PMID: 20971986
Bioinformatics. 2011 Jan 01;27(1):9-13. doi: 10.1093/bioinformatics/btq603. Epub 2010 Oct 22.

MOTIVATION: Next-generation sequencing (NGS) methods have the potential for changing the landscape of biomedical science, but at the same time pose several problems in analysis and interpretation. Currently, there are many commercial and public software packages that analyze NGS...

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Sana ME, Iascone M, Marchetti D, et al. GAMES identifies and annotates mutations in next-generation sequencing projects. Bioinformatics. 2010;27(1):9-13doi: 10.1093/bioinformatics/btq603.
Sana, M. E., Iascone, M., Marchetti, D., Palatini, J., Galasso, M., & Volinia, S. (2011). GAMES identifies and annotates mutations in next-generation sequencing projects. Bioinformatics (Oxford, England), 27(1), 9-13. https://doi.org/10.1093/bioinformatics/btq603
Sana, Maria Elena, et al. "GAMES identifies and annotates mutations in next-generation sequencing projects." Bioinformatics (Oxford, England) vol. 27,1 (2011): 9-13. doi: https://doi.org/10.1093/bioinformatics/btq603
Sana ME, Iascone M, Marchetti D, Palatini J, Galasso M, Volinia S. GAMES identifies and annotates mutations in next-generation sequencing projects. Bioinformatics. 2011 Jan 01;27(1):9-13. doi: 10.1093/bioinformatics/btq603. Epub 2010 Oct 22. PMID: 20971986.
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MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis.

Genome biology

Jia P, Wang Q, Chen Q, Hutchinson KE, Pao W, Zhao Z.
PMID: 25348067
Genome Biol. 2014;15(10):489. doi: 10.1186/s13059-014-0489-9.

Many cancer genes form mutation hotspots that disrupt their functional domains or active sites, leading to gain- or loss-of-function. We propose a mutation set enrichment analysis (MSEA) implemented by two novel methods,MSEA-clust and MSEA-domain, to predict cancer genes based...

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Jia P, Wang Q, Chen Q, et al. MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis. Genome Biol. 2014;15(10):489doi: 10.1186/s13059-014-0489-9.
Jia, P., Wang, Q., Chen, Q., Hutchinson, K. E., Pao, W., & Zhao, Z. (2014). MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis. Genome biology, 15(10), 489. https://doi.org/10.1186/s13059-014-0489-9
Jia, Peilin, et al. "MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis." Genome biology vol. 15,10 (2014): 489. doi: https://doi.org/10.1186/s13059-014-0489-9
Jia P, Wang Q, Chen Q, Hutchinson KE, Pao W, Zhao Z. MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis. Genome Biol. 2014;15(10):489. doi: 10.1186/s13059-014-0489-9. PMID: 25348067; PMCID: PMC4226881.
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Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels.

PloS one

Faircloth BC, Glenn TC.
PMID: 22900027
PLoS One. 2012;7(8):e42543. doi: 10.1371/journal.pone.0042543. Epub 2012 Aug 10.

Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different...

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Faircloth BC, Glenn TC. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One. 2012;7(8):e42543doi: 10.1371/journal.pone.0042543.
Faircloth, B. C., & Glenn, T. C. (2012). Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PloS one, 7(8), e42543. https://doi.org/10.1371/journal.pone.0042543
Faircloth, Brant C, and Glenn, Travis C. "Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels." PloS one vol. 7,8 (2012): e42543. doi: https://doi.org/10.1371/journal.pone.0042543
Faircloth BC, Glenn TC. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One. 2012;7(8):e42543. doi: 10.1371/journal.pone.0042543. Epub 2012 Aug 10. PMID: 22900027; PMCID: PMC3416851.
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Showing 1 to 5 of 5 entries