The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
Open accessAbstract
Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Cited by
Mahapatra, N., Mahanta, P., Pandey, S., & Acharya, R. (2025) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26819 · Cited by 2
Metadata
- Authors
- Coll, F., McNerney, R., Guerra-Assunção, J. A., Glynn, J. R., Perdigão, J., Viveiros, M., Portugal, I., Pain, A., Martin, N., & Clark, T. G.
- Venue
- Nature Communications
- Published
- 2014-09-01
- Volume
- 5
- Issue
- 1
- Pages
- 4812-4812
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2012473911
- Cited by
- 697
- References
- 2
- FWCI
- 21.63
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. https://app.cochat.ai/papers/10.1038/ncomms5812
- The paper
- Coll, F., McNerney, R., Guerra-Assunção, J. A., Glynn, J. R., Perdigão, J., Viveiros, M., Portugal, I., Pain, A., Martin, N., & Clark, T. G. (2014). A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications. https://doi.org/10.1038/ncomms5812
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
