Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

Background: Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a highthroughput laboratory, where hundreds of genes may be targeted in one experiment. Results: We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set o...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Kelvin Li, Anushka Brownley, Timothy B. Stockwell, Karen Beeson, Tina C. McIntosh, Dana Busam, Steve Ferriera, Sean Murphy, Samuel Levy
• Keywords: BMCBI 2008, PCR Primer Design, Primer Design, Target Regions