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Agilent genomics workbench

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Agilent Genomics Workbench is a comprehensive software platform that provides integrated analysis tools for genomic data processing and interpretation. It offers a suite of modules designed to support various workflows in the field of genomics research.

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Agilent Genomic Workbench (14 citations) Agilent Genomics Workbench software (2 citations)

2 protocols using agilent genomics workbench

1

Methylation Analysis of Microarray Data

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Microarray data was quantile normalized using the LIMMA Bioconductor package. Log2 ratios were then imported into Agilent Genomics Workbench (Agilent Technologies), following which the BATMAN algorithm was used to infer the methylation statuses associated with each probe47 (link). Mean methylation states were calculated for probes within a 1,000-bp window and termed a region of interest (ROI). ROIs were then filtered to those with greater than 4 probes and mapped to autosomal chromosomes. ROIs exhibiting a standard deviation greater than 0.65 were used for subgroup assignment as described below. Comparisons between subgroups were performed using a Wilcoxon rank-sum test, and P values were corrected for multiple testing using the Benjamini–Hochberg method. For comparisons of DNA methylation and other factors in this manuscript a Wilcoxon test was used and corrected for multiple testing, such that no assumptions were made regarding the normality of the data distributions.
Mack S.C., Witt H., Piro R.M., Gu L., Zuyderduyn S., Stütz A.M., Wang X., Gallo M., Garzia L., Zayne K., Zhang X., Ramaswamy V., Jäger N., Jones D.T., Sill M., Pugh T.J., Ryzhova M., Wani K.M., Shih D.J., Head R., Remke M., Bailey S.D., Zichner T., Faria C.C., Barszczyk M., Stark S., Seker-Cin H., Hutter S., Johann P., Bender S., Hovestadt V., Tzaridis T., Dubuc A.M., Northcott P.A., Peacock J., Bertrand K.C., Agnihotri S., Cavalli F.M., Clarke I., Nethery-Brokx K., Creasy C.L., Verma S.K., Koster J., Wu X., Yao Y., Milde T., Sin-Chan P., Zuccaro J., Lau L., Pereira S., Castelo-Branco P., Hirst M., Marra M.A., Roberts S.S., Fults D., Massimi L., Cho Y.J., Van Meter T., Grajkowska W., Lach B., Kulozik A.E., von Deimling A., Witt O., Scherer S.W., Fan X., Muraszko K.M., Kool M., Pomeroy S.L., Gupta N., Phillips J., Huang A., Tabori U., Hawkins C., Malkin D., Kongkham P.N., Weiss W.A., Jabado N., Rutka J.T., Bouffet E., Korbel J.O., Lupien M., Aldape K.D., Bader G.D., Eils R., Lichter P., Dirks P.B., Pfister S.M., Korshunov A, & Taylor M.D. (2014). Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature, 506(7489), 445-450.
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2

Comprehensive Genomic Analysis of Patients

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The a-CGH analysis was performed by using Agilent SurePrint G3 CGH+SNP Microarray Kit (4x180K) (Agilent Technologies, Inc., Santa Clara, CA, USA). Data analysis was performed using Agilent Genomics Workbench (v5.0.2.5). Genomic linear positions were given relative to hg19. The deleted genomic regions of the patients were evaluated using some specific databases such as Online Mendelian Inheritance in Man (https://www.omim.org), The Database of Genomic Variants (DGV, http://dgv.tcag.ca/dgv/app/home), The DatabasE of genomiC varIations and Phenotype in Humans using Ensembl Resources (DECIPHER, https://decipher.sanger.ac.uk), and DISEASES (https://diseases.jensenlab.org/Search).
Sharifi S., Kalaycı T., Palanduz Ş., Öztürk Ş, & Cefle K. (2021). Clinical Characteristics and Mutation Spectrum of Neurofibromatosis Type 1 in 27 Turkish Families. Balkan Medical Journal, 38(6), 365-373.
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