Analysis of array-CGH data using the R and Bioconductor software suite.
BACKGROUND
Array-based comparative genomic hybridization (array-CGH) is an emerging high-resolution and high-throughput molecular genetic technique that allows genome-wide screening for chromosome alterations. DNA copy number alterations (CNAs) are a hallmark of somatic mutations in tumor genomes and congenital abnormalities that lead to diseases such as mental retardation. However, accurate identification of amplified or deleted regions requires a sequence of different computational analysis steps of the microarray data.


RESULTS
We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs.


CONCLUSIONS
The implemented option for the determination of minimal altered regions (MARs) from a series of tumor samples is a step forward in the identification of new tumor suppressor genes or oncogenes.
Hofmann
Winfried A
WA
Hannover Medical School, Institute of Cell and Molecular Pathology, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
Weigmann
Anja
A
Tauscher
Marcel
M
Skawran
Britta
B
Focken
Tim
T
Buurman
Reena
R
Wingen
Luzie U
LU
Schlegelberger
Brigitte
B
Steinemann
Doris
D
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