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. 2022 Jul 5;23(1):147.
doi: 10.1186/s13059-022-02714-x.

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Martin Hunt  1   2 , Brice Letcher  1 , Kerri M Malone  1 , Giang Nguyen  1 , Michael B Hall  1 , Rachel M Colquhoun  3 , Leandro Lima  1 , Michael C Schatz  4 , Srividya Ramakrishnan  4 ; CRyPTIC consortium; Zamin Iqbal  5
Affiliations

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Martin Hunt et al. Genome Biol. .

Abstract

There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).

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Conflict of interest statement

E.R. is employed by the UK Health Security Agency and holds an honorary contract with Imperial College London. I.F.L. is Director of the Scottish Mycobacteria Reference Laboratory. S.N. receives funding from German Center for Infection Research, Excellenz Cluster Precision Medicine in Chronic Inflammation, Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG)tion EXC 2167. P.S. is a consultant at Genoscreen. T.R. is funded by NIH and DoD and receives salary support from the non-profit organization FIND. T.R. is a co-founder, board member and shareholder of Verus Diagnostics Inc, a company that was founded with the intent of developing diagnostic assays. Verus Diagnostics was not involved in any way with data collection, analysis, or publication of the results. T.R. has not received any financial support from Verus Diagnostics. UCSD Conflict of Interest office has reviewed and approved T.R.’s role in Verus Diagnostics Inc. T.R. is a co-inventor of a provisional patent for a TB diagnostic assay (provisional patent #: 63/048.989). T.R. is a co-inventor on a patent associated with the processing of TB sequencing data (European Patent Application No. 14840432.0 & USSN 14/912,918). T.R. has agreed to “donate all present and future interest in and rights to royalties from this patent” to UCSD to ensure that he does not receive any financial benefits from this patent. S.S. is working and holding ESOPs at HaystackAnalytics Pvt. Ltd. (Product: Using whole genome sequencing for drug susceptibility testing for Mycobacterium tuberculosis). G.F.G. is listed as an inventor on patent applications for RBD-dimer-based CoV vaccines. The patents for RBD-dimers as protein subunit vaccines for SARS-CoV-2 have been licensed to Anhui Zhifei Longcom Biopharmaceutical Co. Ltd, China.

Figures

Fig. 1
Fig. 1
Variant adjudication pipeline implemented by Minos. Input variants in one or more VCF file(s) are merged to make a deduplicated set of variants. When running on a single sample, the input VCF files could be from different tools. When joint genotyping across samples, there is one VCF file originating from each sample. Next, overlapping variants are clustered together—for example the variants at positions 7 and 8—allowing the construction of a non-nested variation graph. Genotype calls are made using read mapping to the graph
Fig. 2
Fig. 2
Precision and recall when joint genotyping M. tuberculosis outbreak data. The left plot considers non-reference allele calls only, i.e., the variant sites that are genotyped to be different from the reference genome. The right plot shows the results when all allele calls are included. Individual samples are marked as dots, and the mean precision and recall for each tool is shown as a cross. The convex hull of the data points for each caller is shaded with an associated color
Fig. 3
Fig. 3
All amino acid variants identified in the RRDR of the rpoB gene by joint genotyping 8,955 samples from the CRyPTIC M. tuberculosis data set. Each plot shows the RRDR region from left to right. Single amino acid variants are shown in the upper grid, with the y axis corresponding to the variant amino acid. The lower area shows deletions and insertions, with the inserted sequence given in the colored boxes. For example, the leftmost deletion of amino acids TS at position 427-428 is found in one sample, which is resistant. The leftmost insertion adds R after the S at position 431 (found in one resistant sample). The plots show the same variants, but with different color schemes. In a each variant is colored by the number of samples possessing that variant. Plot b colors the variants by the percent of samples with that variant that are rifampicin resistant
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