Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2008;1(4):368-95.
doi: 10.1504/IJCBDD.2008.022208.

Statistical issues in the analysis of DNA Copy Number Variations

Nathan E Wineinger  1 , Richard E Kennedy, Stephen W Erickson, Mary K Wojczynski, Carl E Bruder, Hemant K Tiwari
Affiliations
Review

Statistical issues in the analysis of DNA Copy Number Variations

Nathan E Wineinger et al. Int J Comput Biol Drug Des. 2008.

Abstract

Approaches to assess copy number variation have advanced rapidly and are being incorporated into genetic studies. While the technology exists for CNV genotyping, a further understanding and discussion of how to use the CNV data for association analyses is warranted. We present the options available for processing and analysing CNV data. We break these steps down into choice of genotyping platform, normalisation of the array data, calling algorithm, and statistical analysis.

Keywords: CBS; DNA; GWAS; array CGH; calling algorithm; circular binary segmentation; complex disorders; copy number; genome-wide association study; hidden Markov model; microarray; normalization; whole genome amplification.

PubMed Disclaimer

References

    1. Affymetrix (2008) Affymetrix® Genotyping Console™ Software.

    1. Andersson R, Bruder CE, Piotrowski A, Menzel U, Nord H, Sandgren J, Hvidsten TR, Diaz de Ståhl T, Dumanski JP, Komorowski JA. Segmental maximum a posteriori approach to genome-wide copy number profiling. Bioinformatics. 2008 15 March;24(6):751–758. - PubMed
    1. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 22 January;19(2):185–193. - PubMed
    1. Bolstad BM, Irizarry RA, Gautie L, Wu Z. Preprocessing high-density oligonucleotide arrays. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors. Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer; New York: 2005. pp. 13–32.
    1. Broët P, Richardson S. Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model. Bioinformatics. 2006 15 April;22(8):911–918. - PubMed

Publication types