论文信息 - Breakpoint identification and smoothing of array comparative genomic hybridization data

Breakpoint identification and smoothing of array comparative genomic hybridization data

SUMMARY We describe a tool, called aCGH-Smooth, for the automated identification of breakpoints and smoothing of microarray comparative genomic hybridization (array CGH) data. aCGH-Smooth is written in visual C++, has a user-friendly interface including a visualization of the results and user-defined parameters adapting the performance of data smoothing and breakpoint recognition. aCGH-Smooth can handle array-CGH data generated by all array-CGH platforms: BAC, PAC, cosmid, cDNA and oligo CGH arrays. The tool has been successfully applied to real-life data. AVAILABILITY aCGH-Smooth is free for researchers at academic and non-profit institutions at http://www.few.vu.nl/~vumarray/.

[1] D. Pinkel,et al. Genome wide array comparative genomic hybridisation analysis of premalignant lesions of the stomach , 2003, Molecular pathology : MP.

[2] W. Kuo,et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays , 1998, Nature Genetics.

[3] Elena Marchiori,et al. Chromosomal Breakpoint Detection in Human Cancer , 2003, EvoWorkshops.

[4] Christian A. Rees,et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[5] Ajay N. Jain,et al. Fully automatic quantification of microarray image data. , 2002, Genome research.

[6] Jaakko Astola,et al. CGH-Plotter: MATLAB toolbox for CGH-data analysis , 2003, Bioinform..