Towards better prediction of Mycobacterium tuberculosis lineages from MIRU-VNTR data.

ABSTRACT: The determination of lineages from strain-based molecular genotyping information is an important problem in tuberculosis. Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is a commonly used molecular genotyping approach that uses counts of the number of times pre-specified loci repeat in a strain. There are three main approaches for determining lineage based on MIRU-VNTR data - one based on a direct comparison to the strains in a curated database, and two others, on machine learning algorithms trained on a large collection of labeled data. All existing methods have limitations. The direct approach imposes an arbitrary threshold on how much a database strain can differ from a given one to be informative. On the other hand, the machine learning-base

SUBMITTER: Thain N 

PROVIDER: S-EPMC6708508 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature