VU Micro-Array Data Analysis

This site will be used to make our data analysis tools publicly available. Currently only one tool is available, but there will be more in the (near) future.

aCGH-Smooth

aCGH-Smooth is a tool for the analysis of array Comparative Genomic Hybridization (array-CGH) data.

Array-CGH is nowadays the method of choice for studying DNA copy number changes because of its high sensitivity and resolution. The chromosomal copy numbers of the actual tumor cells are detected relative to a normal reference sample. The ratios found in the experiment have some "noise" generated by polymorphic sites (sequence variation between individuals), some experimental noise as well as compression of the ratios due to admixed normal cells in the tumor sample.

aCGH-Smooth is written in visual C++. It has a user-friendly interface including a visualization of the results, which highlights the obtained smoothing and allows the user to influence the smoothing and number of breakpoints by setting the value of suitable parameters. A-CGH smooth is suitable for CGH data generated by BAC, PAC, cosmid, cDNA and oligo CGH arrays. It facilitates data interpretation and is an superior alternative to smoothing the data using a "moving average".

aCGH-Smooth employs a "smoothing" algorithm that adjusts the observed array-CGH values such that they represent the copy number of the most common tumor cells.

Warning

The tool is freely available to researchers at academic and non-profit institutions. This program is distributed WITHOUT ANY WARRANTY.

Update Information

If you want to be informed about updates, please send your e-mail address to Bauke Ylstra

Download

When downloading the following files you may have to right-click on the link and select "save link" or "save target as" from the menu.

aCGH-Smooth.exe (update 11-5-2004)
aCGH-Smooth.hlp (Please place this file in same directory as executable)
example of input file.

Help

On-line version of help

Installation notes

You can place the executable file (acghsmooth.exe) wherever you want on your hard-disk. However, please make sure you place the help file (acghsmooth.hlp) in the same directory as the executable.

Contact

For further information, problems, bugs etc. please contact Kees Jong.

References

K. Jong, E. Marchiori, A. van der Vaart, B. Ylstra, G. Meijer, M, Weiss. Chromosomal Breakpoint Detection in Human Cancer. In Applications of Evolutionary Computing. EvoBIO: Evolutionary Computation and Bioinformatics. Springer LNCS 2611, pp. 54-65, 2003.
K. Jong, E. Marchiori, A. van der Vaart, G. Meijer, B. Ylstra. Automatic Breakpoint Identification and Smoothing of Array Comparative Genomic Hybridization Data. Bioinformatics, 2004.