Analysis of molecular inversion probe performance for allele copy number determination

Yuker Wang^*¹ , Martin Moorhead^*¹ , 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

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

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

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

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R246doi:10.1186/gb-2007-8-11-r246


Published:	20 November 2007

Subject areas: Genome studies, Methods, Molecular biology

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.