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Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization

John C Marioni, Natalie P Thorne, Armand Valsesia, Tomas Fitzgerald, Richard Redon, Heike Fiegler, T Daniel Andrews, Barbara E Stranger, Andrew G Lynch, Emmanouil T Dermitzakis, Nigel P Carter, Simon Tavaré and Matthew E Hurles*

Genome Biology 2007, 8:R228  doi:10.1186/gb-2007-8-10-r228

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Data "waves" in SNP array data

Kylie Louise Gorringe   (2008-07-01 19:17)  Peter MacCallum Cancer Centre email

We sometimes observe data "waves" in our Affy SNP array copy number data. It is inconsistent between samples or experimental batches and sometimes a second DNA prep or extra clean-up of the same sample removes the effect. It seems to be more common in whole-genome amplified DNA or DNA from limited sources (eg tumour biopsies). I'd be interested to know if anyone has identified why this occurs or has a solution for analysing tumor data.

Competing interests

None declared


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