MinorityReport, software for generalized analysis of causal genetic variants
Horst JA, Wu W, DeRisi JLMalaria Journal, 2017Abstract:
Background: The widespread availability of next generation genome sequencing technologies has enabled a wide
range of variant detection applications, especially in cancer and inborn genetic disorders. For model systems and
microorganisms, the same technology may be used to discover the causative mutations for any phenotype, including
those generated in response to chemical perturbation. In the case of pathogenic organisms, these approaches have
allowed the determination of drug targets by means of resistance selection followed by genome sequencing.
Results: MinorityReport is open source software written in python that facilitates the comparison of any two sets of
genome alignments for the purpose of rapidly identifying the spectrum of nonsynonymous changes, insertions or
deletions, and copy number variations in a presumed mutant relative to its parent. Specifically, MinorityReport relates
mapped sequence reads in SAM format output from any alignment tool for both the mutant and parent genome,
relative to a reference genome, and produces the set of variants that distinguishes the mutant from the parent, all
presented in an intuitive, straightforward report format. MinorityReport features tunable parameters for evaluating
evidence and a scoring system that prioritizes reported variants based on relative proportions of read counts supporting
the variant in the mutant versus parent data sets. The utility of MinorityReport is demonstrated using previously
published publicly available data sets to find the determinants of resistance for novel anti-malarial drugs.
Conclusions: MinorityReport is readily available (github: JeremyHorst/MinorityReport) to identify the genetic mechanisms
of drug resistance in Plasmodium, genotype-phenotype relationships in human diads, or genomic variations
between any two related organisms.