title: Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis.
abstract: When using genome sequencing for molecular epidemiology, short sequence reads are aligned to an arbitrary reference strain to detect single nucleotide polymorphisms. We investigated whether reference genome selection influences epidemiological inferences of Mycobacterium tuberculosis transmission by aligning sequence reads from 162 closely related lineage 4 (Euro-American) isolates to 7 different genomes. Phylogenetic trees were consistent with use of all but the most divergent genomes, suggesting that reference choice can be based on considerations other than M. tuberculosis lineage.
authors.affiliation: McGill University, Department of Epidemiology, Biostatistics and Occupational Health, Montreal, Canada.|The Research Institute of the McGill University Health Centre, Montreal, Canada.|McGill International TB Centre, Montreal, Canada.
authors.forename: Robyn S
authors.initials: RS
authors.lastname: Lee
authors.affiliation: The Research Institute of the McGill University Health Centre, Montreal, Canada marcel.behr@mcgill.ca.|McGill International TB Centre, Montreal, Canada.|McGill University Health Centre, Department of Medicine, Division of Infectious Diseases, Montreal, Canada.
authors.forename: Marcel A
authors.initials: MA
authors.lastname: Behr
mesh_terms: D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods*; D058889:Molecular Typing / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014376:Tuberculosis / Q000175:diagnosis* / Q000453:epidemiology*