Genome Biology Volume 8 Issue 10

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Data "waves" in SNP array data

Kylie Louise Gorringe   (01 July 2008)  Peter MacCallum Cancer Centre

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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