Resolution in forensic microbial genotyping

Velsko, S P

Lawrence Livermore National Laboratory

关键词: Modifications;    Mathematical Models;    59 Basic Biological Sciences;    Mutations;    Design;   

DOI  :  10.2172/883607
RP-ID  :  UCRL-TR-215305
RP-ID  :  W-7405-ENG-48
RP-ID  :  883607

美国|英语

来源: UNT Digital Library

【 摘 要 】

Resolution is a key parameter for differentiating among the large number of strain typing methods that could be applied to pathogens involved in bioterror events or biocrimes. In this report we develop a first-principles analysis of strain typing resolution using a simple mathematical model to provide a basis for the rational design of microbial typing systems for forensic applications. We derive two figures of merit that describe the resolving power and phylogenetic depth of a strain typing system. Rough estimates of these figures-of-merit for MLVA, MLST, IS element, AFLP, hybridization microarrays, and other bacterial typing methods are derived from mutation rate data reported in the literature. We also discuss the general problem of how to construct a ''universal'' practical typing system that has the highest possible resolution short of whole-genome sequencing, and that is applicable with minimal modification to a wide range of pathogens.