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Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference

https://doi.org/10.1101/733642
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1110s43openalex-snapshot
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.cmi.2019.03.022openalex-snapshot
Role and value of whole genome sequencing in studying tuberculosis transmission
inferredcites →https://doi.org/10.1016/s1473-3099(12)70277-3openalex-snapshot
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
inferredcites →https://doi.org/10.1016/s1473-3099(15)00062-6openalex-snapshot
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study
inferredcites →https://doi.org/10.1016/s1473-3099(15)00499-5openalex-snapshot
The transmission of Mycobacterium tuberculosis in high burden settings
inferredcites →https://doi.org/10.1016/s1473-3099(18)30218-4openalex-snapshot
Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis
inferredcites →https://doi.org/10.1016/s2213-2600(14)70027-xopenalex-snapshot
Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007–12, with whole pathogen genome sequences: an observational study
inferredcites →https://doi.org/10.1016/s2213-2600(19)30137-7openalex-snapshot
Paediatric tuberculosis transmission outside the household: challenging historical paradigms to inform future public health strategies
inferredcites →https://doi.org/10.1038/nbt.2835openalex-snapshot
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
inferredcites →https://doi.org/10.1038/nbt.4235openalex-snapshot
A universal SNP and small-indel variant caller using deep neural networks
inferredcites →https://doi.org/10.1038/ncomms10063openalex-snapshot
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1038/ncomms11465openalex-snapshot
Correction: Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1038/ng.2656openalex-snapshot
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
inferredcites →https://doi.org/10.1038/s41579-019-0214-5openalex-snapshot
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
inferredcites →https://doi.org/10.1038/s41587-019-0054-xopenalex-snapshot
Best practices for benchmarking germline small-variant calls in human genomes
inferredcites →https://doi.org/10.1038/s41587-019-0074-6openalex-snapshot
An open resource for accurately benchmarking small variant and reference calls
inferredcites →https://doi.org/10.1038/s41588-018-0117-9openalex-snapshot
Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam
inferredcites →https://doi.org/10.1038/s41598-018-23276-8openalex-snapshot
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction
inferredcites →https://doi.org/10.1038/s41598-018-33731-1openalex-snapshot
Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase
inferredcites →https://doi.org/10.1038/s41598-019-41967-8openalex-snapshot
Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting
inferredcites →https://doi.org/10.1038/srep42814openalex-snapshot
Genetic diversity, transmission dynamics and drug resistance of Mycobacterium tuberculosis in Angola
inferredcites →https://doi.org/10.1056/nejmoa1604544openalex-snapshot
Transmission of Extensively Drug-Resistant Tuberculosis in South Africa
inferredcites →https://doi.org/10.1056/nejmra021964openalex-snapshot
Molecular Epidemiology of Tuberculosis
inferredcites →https://doi.org/10.1093/bioinformatics/btp373openalex-snapshot
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
inferredcites →https://doi.org/10.1093/bioinformatics/btr509openalex-snapshot
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/bioinformatics/bty633openalex-snapshot
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
inferredcites →https://doi.org/10.1093/bioinformatics/btz305openalex-snapshot
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
inferredcites →https://doi.org/10.1093/infdis/jiw014openalex-snapshot
Within-Host Heterogeneity ofMycobacterium tuberculosisInfection Is Associated With Poor Early Treatment Response: A Prospective Cohort Study
inferredcites →https://doi.org/10.1093/infdis/jix362openalex-snapshot
What We Know About Tuberculosis Transmission: An Overview
inferredcites →https://doi.org/10.1093/molbev/msu121openalex-snapshot
Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data
inferredcites →https://doi.org/10.1093/molbev/msw124openalex-snapshot
Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
inferredcites →https://doi.org/10.1093/molbev/msw275openalex-snapshot
Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks
inferredcites →https://doi.org/10.1093/molbev/msy242openalex-snapshot
Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions
inferredcites →https://doi.org/10.1099/mgen.0.000056openalex-snapshot
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
inferredcites →https://doi.org/10.1099/mgen.0.000060openalex-snapshot
Declaring a tuberculosis outbreak over with genomic epidemiology
inferredcites →https://doi.org/10.1099/mgen.0.000217openalex-snapshot
Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission
inferredcites →https://doi.org/10.1099/mgen.0.000219openalex-snapshot
Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population
inferredcites →https://doi.org/10.1099/mgen.0.000261openalex-snapshot
Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP
inferredcites →https://doi.org/10.1101/403824openalex-snapshot
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
inferredcites →https://doi.org/10.1111/1755-0998.12676openalex-snapshot
treespace : Statistical exploration of landscapes of phylogenetic trees
inferredcites →https://doi.org/10.1128/cmr.00021-12openalex-snapshot
Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control
inferredcites →https://doi.org/10.1128/cmr.00061-05openalex-snapshot
Molecular Epidemiology of Tuberculosis: Current Insights
inferredcites →https://doi.org/10.1128/jcm.00025-15openalex-snapshot
PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data
inferredcites →https://doi.org/10.1128/jcm.00364-16openalex-snapshot
Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis
inferredcites →https://doi.org/10.1136/bmjopen-2012-002468openalex-snapshot
A retrospective cohort study: 10-year trend of disease-modifying antirheumatic drugs and biological agents use in patients with rheumatoid arthritis at Veteran Affairs Medical Centers
inferredcites →https://doi.org/10.1186/1471-2334-13-1openalex-snapshot
Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis
inferredcites →https://doi.org/10.1186/1471-2334-13-110openalex-snapshot
Inferring patient to patient transmission of Mycobacterium tuberculosisfrom whole genome sequencing data
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1186/s12859-018-2151-0openalex-snapshot
Identification of missing variants by combining multiple analytic pipelines
inferredcites →https://doi.org/10.1186/s12859-018-2201-7openalex-snapshot
Recommending plant taxa for supporting on-site species identification
inferredcites →https://doi.org/10.1186/s12864-015-2294-6openalex-snapshot
Locating rearrangement events in a phylogeny based on highly fragmented assemblies
inferredcites →https://doi.org/10.1186/s12864-016-2467-yopenalex-snapshot
Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
inferredcites →https://doi.org/10.1186/s12916-015-0545-7openalex-snapshot
Cancer and fertility preservation: international recommendations from an expert meeting
inferredcites →https://doi.org/10.1186/s12916-016-0566-xopenalex-snapshot
Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review
inferredcites →https://doi.org/10.1186/s12916-018-1111-xopenalex-snapshot
Investigating spillover of multidrug-resistant tuberculosis from a prison: a spatial and molecular epidemiological analysis
inferredcites →https://doi.org/10.1186/s13073-015-0164-0openalex-snapshot
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
inferredcites →https://doi.org/10.1371/journal.pcbi.1003457openalex-snapshot
Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
inferredcites →https://doi.org/10.1371/journal.pmed.1001387openalex-snapshot
Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study
inferredcites →https://doi.org/10.1371/journal.pone.0122979openalex-snapshot
Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome
inferredcites →https://doi.org/10.1371/journal.pone.0131080openalex-snapshot
Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps
inferredcites →https://doi.org/10.1371/journal.pone.0139047openalex-snapshot
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
inferredcites →https://doi.org/10.1371/journal.pone.0212817openalex-snapshot
Maternal anemia and birth weight: A prospective cohort study
inferredcites →https://doi.org/10.1371/journal.ppat.1006885openalex-snapshot
When are pathogen genome sequences informative of transmission events?
inferredcites →https://doi.org/10.1371/journal.ppat.1008067openalex-snapshot
The molecular clock of Mycobacterium tuberculosis
inferredcites →https://doi.org/10.3389/fgene.2015.00001openalex-snapshot
Hereditary hemorrhagic telangiectasia: genetics and molecular diagnostics in a new era
inferredcites →https://doi.org/10.3389/fgene.2015.00235openalex-snapshot
Best practices for evaluating single nucleotide variant calling methods for microbial genomics
inferredcites →https://doi.org/10.4269/ajtmh.17-0480openalex-snapshot
Genetic Clustering of Tuberculosis in an Indigenous Community of Brazil
inferredcites →https://doi.org/10.7554/elife.05166openalex-snapshot
Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area
inferredcites →https://doi.org/10.7717/peerj.5895openalex-snapshot
MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.meegid.2019.104152openalex-snapshot
An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data
inferred← citeshttps://doi.org/10.1111/mmi.14409openalex-snapshot
New insights into the mycobacterial PE and PPE proteins provide a framework for future research
inferred← citeshttps://doi.org/10.1128/spectrum.02244-22openalex-snapshot
Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area
inferred← citeshttps://doi.org/10.3390/microorganisms8050667openalex-snapshot
Mycobacterium bovis: From Genotyping to Genome Sequencing
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