Decision Networks to enhance HIV drug resistance prediction
Sint-Martens-Latem, Belgium, January 10, 2008 – Applied Maths NV today announces the release of a new Plugin tool for high-throughput HIV drug resistance prediction, running on version 5.1 of its flagship software suite BioNumerics.
HIV drug resistance screening based on de novo sequencing of the HIV-1 pol gene, is common practice in hospitals and clinical laboratories. A number of well-described SNPs on the viral protease, reverse transcriptase and integrase protein sequences are responsible for resistance towards specific HIV drugs. These SNPs often interact with each other in a complex manner, inducing increased resistance or susceptibility towards specific drugs. Public and proprietary databases are available, containing rule-based drug resistance schemes (algorithms), predicting drug resistances based on specific SNPs (e.g., the Stanford HIVDB database). However, resistance rules are often trapped in closed systems, not revealing which SNPs or combinations are causative of resistance. Within the BioNumerics® environment, Applied Maths has developed an open expert system that allows one to create and (re)evaluate own and/or publicly available expert rules. XML-formatted algorithm rules are parsed within the BioNumerics® software and converted automatically into Decision Networks. The advantages of Decision Networks over other approaches are diverse: (1) Any set of rules, based on public or proprietary algorithms can be imported and applied in combination with other algorithms; (2) Since drug predictions usually are the result of a complex combination of individual rules, in critical cases it can be life-saving to evaluate the rules that have led to a specific decision. Based upon that knowledge, the specialist can determine the optimal combination of drugs to be applied; (3) BioNumerics’ Decision Networks can be refined and extended by the user based upon newly acquired knowledge and insights, or may be used as a research tool to test new working hypotheses. Similar Decision Networks can easily be created for other applications in virology, epidemiology, microbiology or diagnostics.
The automated approach offered by BioNumerics allows for high-throughput drug resistance screening of sampled HIV sequences. Drug resistance predictions are reported per patient, for a set of patients, or for a single patient followed over time. Based on these reports, optimal drugs for HAART (Highly Active Antiretroviral Therapy) can be selected. BioNumerics’ rich database environment allows for storage of all information about the patient as well as clinical information such as CD4 counts, viral load evolutions, etc., assisting in improved patient management.
About Applied Maths
Applied Maths, a bioinformatics company, was set up in 1992 and incorporated in 1994. Since then, it has gained global recognition with its software for the analysis of electrophoresis patterns. The company has acquired a unique market position with BioNumerics, a software suite for integrated databasing and the analysis of all kinds of biodata. BioNumerics has developed into a multi-faceted platform combining databasing and analysis technologies, with numerous applications in research and diagnostics, including in bacterial and viral epidemiology and profiling, plant improvement, human genetics and biotechnology.
Applied Maths combines extensive expertise in bioinformatics and unique mathematical know-how to develop the most powerful and fastest algorithms for pattern recognition and matching, data mining, screening and clustering. In so doing, the company fulfils a critical requirement in the bioinformatics industry for obtaining and analysing greater and more complex data sets. The impact of Applied Maths' software is evidenced by referrals in more than 1300 scientific publications and an impressive portfolio of customers in the academic, industrial, clinical and public sectors in more that eighty countries throughout the world. The BioNumerics software platform is used in many prestigious international projects and networks.
In 2006 Applied Maths has entered into a financial partnership with KBC Private Equity and KBC Private Equity Fund Biotech. Applied Maths has units in Sint-Martens-Latem (Belgium) (head office) and Austin (USA). For further information, please visit the company's website: www.applied-maths.com.