A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and de

Background: Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nucleotide polymorphism arrays. One of the methods compared is our non-homogenous Hidden Markov Model approach. Our approach uses Markov Chain Monte Carlo for inference, but Yu et al. ran the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state. Methods: We rerun the analysis in Yu et al. using appropriate settings for both the Markov Chain Monte Carlo iterations and the reference level. Additionally, to show how easy it is to obtain answers to additional specific questions, we have added a new analysis targeted specifically to the detection of breakpoints. Results: The reanalysis shows that the performance of our method is comparable to t...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Oscar M. Rueda, Ramón Díaz-Uriarte
• Keywords: BMCBI 2007, Markov Chain Monte, Markov Chain Monte Carlo, Single Nucleotide Polymorphism