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Hofmann WA, Weigmann A, Tauscher M, et al. Analysis of array-CGH data using the R and Bioconductor software suite. Comp Funct Genomics. 2009;201325doi: 10.1155/2009/201325.
Hofmann, W. A., Weigmann, A., Tauscher, M., Skawran, B., Focken, T., Buurman, R., Wingen, L. U., Schlegelberger, B., & Steinemann, D. (2009). Analysis of array-CGH data using the R and Bioconductor software suite. Comparative and functional genomics, 201325. https://doi.org/10.1155/2009/201325
Hofmann, Winfried A, et al. "Analysis of array-CGH data using the R and Bioconductor software suite." Comparative and functional genomics vol. (2009): 201325. doi: https://doi.org/10.1155/2009/201325
Hofmann WA, Weigmann A, Tauscher M, Skawran B, Focken T, Buurman R, Wingen LU, Schlegelberger B, Steinemann D. Analysis of array-CGH data using the R and Bioconductor software suite. Comp Funct Genomics. 2009;201325. doi: 10.1155/2009/201325. Epub 2009 Aug 19. PMID: 19696946; PMCID: PMC2728899.
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Comp Funct Genomics. 2009;201325. doi: 10.1155/2009/201325. Epub 2009 Aug 19.

Analysis of array-CGH data using the R and Bioconductor software suite.

Comparative and functional genomics

Winfried A Hofmann, Anja Weigmann, Marcel Tauscher, Britta Skawran, Tim Focken, Reena Buurman, Luzie U Wingen, Brigitte Schlegelberger, Doris Steinemann

Affiliations

  1. Hannover Medical School, Institute of Cell and Molecular Pathology, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.

PMID: 19696946 PMCID: PMC2728899 DOI: 10.1155/2009/201325

Abstract

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.

CONCLUSION: 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.

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