Computational tradeoffs in multiplex PCR assay design for SNP genotyping.docVIP

BMC Genomics BioMedCentral Research article Open Access Computational tradeoffs in multiplex PCR assay design for SNP genotyping John Rachlin*1, Chunming Ding2, Charles Cantor1,3,4,6 and Simon Kasif1,3,5 Address: 1Bioinformatics program, Boston University, Boston MA 02215, USA, 2Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region, Hong Kong, 3Department of Biomedical Engineering, Boston University, MA 02215, USA, 4Center for Advanced Biotechnology, Boston University, MA 02215, USA, 5Center for Advanced Genomic Technologies, Boston University, MA 02215, USA and 6SEQUENOM, Inc., San Diego, CA 92121-1331, USA Email: John Rachlin* - rachlin@; Chunming Ding - cmding@.hk; Charles Cantor - ccantor@; Simon Kasif - kasif@ * Corresponding author Published: 25 July 2005 Received: 28 March 2005 Accepted: 25 July 2005 BMC Genomics 2005, 6:102 doi:10.1186/1471-2164-6-102 This article is available from: /1471-2164/6/102 ? 2005 Rachlin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Multiplex PCR is a key technology for detecting infectious microorganisms, whole- genome sequencing, forensic analysis, and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR assays requires the consideration of multiple competing objectives and physical constraints, and extensive computational analysis must be performed in order to identify the possible formation of primer-dimers that can negatively impact product yield. Results: This paper examines the computational design limits of multiplex PCR in the context of SNP genotyping and examines tradeoffs ass