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March 2007, SoftGenetics -Hypervariable Mutation Detection with Mutation Surveyor ®:


Organisms contain areas in the genome with hypervariability. Abacteriophage that infects Bordetella bronchiseptica, a relative of the bacterium that causes whooping cough, contains genes to specifically change its proteins thus permitting binding to different cell receptors (1). These genes allow the phage to rapidly evolvenew variants that can recognize and attack bacteria that may have become resistant to the previous phage. Similarly, infection by the influenza virus requires receptor binding through cell-specific tropism (2). Several strains of Helicobacter pylori, the organism responsible for many cases of peptic ulcers and stomach cancer, show antibiotic resistance possibly due to efficiency ofDNA repair or DNA polymerase (3). Additional causes for high mutation frequency come from antigenic variation found in sexually transmitted HIV (4) and the development of drug resistance mutations as in the case of the blood borne pathogen Hepatitis C virus (HCV). Projects involving a high level of variability demand fully automated calls of SNPs and homozygous and heterozygous indels to identify variance between strains. Mutation Surveyor and Mutation Explorer are the only software packages that detect heterozygous indels by deconvoluting DNA sequence traces. Mutation Surveyorand Mutation Explorer also provide an accuracy >99% in detecting homozygous and heterozygous SNPs (5), when both forward and reverse traces are of Ph red 20 quality. Both packages feature ease of use, low-learning curve, full automation, and an exclusive migration time comparison to detect Indels.


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