Phylogenetic Analysis Software

Development of a Phylogenetic Analysis Software for the Evaluation of Genetic Data Derived Using the Triangulation Identification for Genetic Evaluation of Risk (TIGER) Platform

Triangulation Identification for the Evaluation of Risk (TIGER) is a genetic analysis system developed by our collaborators, [IBIS Pharmaceuticals www.ibisbiosciences.com] (Carlsbad, Ca) for use by the military’s bioterrorism task force. In general TIGER uses PCR (polymerase chain reaction) to amplify select regions of an infectious microbial genome. The amplicons are purified by chromatographic methods, and analyzed by mass spectrometry. By determining the mass of the PCR product, the base composition of each PCR amplicon can be determined within a one base pair mutation. TIGER is able to provide information regarding antimicrobial resistance, identification, and virulence. TIGER has become one of the most advanced systems for molecular diagnostics and provides information that previously was only available via whole genome sequencing. Recently we have been using the TIGER technology to study the molecular epidemiology of pathogens such as Methicillin Resistant Staphylococcus aureus and Acinetobacter baumanni. Traditionally phylogenetic analysis begins with the alignment of two or more DNA sequences. Algorithms such as BLAST (Basic Local Alignment Search Tool) and ClustalW align DNA sequences and report the genetic distance using the equations D = p / 2 and p = (d/tb) *100 respectively, where D is genetic distance, p is percent similarity; d is the summation of the differences in base pairs, and tb is the total number of bases in the genes examined. TIGER, however does not produce sequence data. Instead it produces a one dimensional matrix in which the elements represent the respective base compositions. In order to do phylogentic analysis using TIGER data, the number of total bases is determined by taking a sum of the respective base compositions. This is then used to determine the presence of deletion mutations. Furthermore, the numbers of the individual nitrogenous bases are used to determine the presence of substitution mutations. From this data the genetic distance can be calculated, and is then used to construct a dendragram to show phylogenetic relationships. As of now phylogenetic analysis using TIGER data is cumbersome and is usually done by hand. This project will attempt to design a program that can do such a phylogenetic analysis in a more timely fashion. The resulting program will allow for more rapid assessment of molecular epidemiological data. Such a program will greatly enhance the study of molecular epidemiology using the TIGER system.