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Open Access Method

Analysis of molecular inversion probe performance for allele copy number determination

Yuker Wang1, Martin Moorhead1, George Karlin-Neumann1, Nicholas J Wang2, James Ireland1, Steven Lin1, Chunnuan Chen1, Laura M Heiser2, Koei Chin3, Laura Esserman3, Joe W Gray2, Paul T Spellman2* and Malek Faham1*

Author Affiliations

1 Affymetrix Inc., Shoreline Blvd, South San Francisco, CA 94080, USA

2 LBL 1 Cyclotron Rd, MS977R225A, Berkeley, CA 94720, USA

3 Comprehensive Cancer Center, Sutter Street, University of California San Francisco, San Francisco, CA 94143, USA

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Genome Biology 2007, 8:R246  doi:10.1186/gb-2007-8-11-r246

Published: 20 November 2007

Abstract

We have developed a new protocol for using molecular inversion probes to accurately and specifically measure allele copy number. The new protocol provides for significant improvements, including the reduction of input DNA (from 2 μg) by more than 25-fold (to 75 ng total genomic DNA), higher overall precision resulting in one order of magnitude lower false positive rate, and greater dynamic range with accurate absolute copy number up to 60 copies.