The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
Spatial genomics maps the structure, nature and evolution of cancer clones
Open accessAbstract
Genome sequencing of cancers often reveals mosaics of different subclones present in the same tumour 1–3. Although these are believed to arise according to the principles of somatic evolution, the exact spatial growth patterns and underlying mechanisms remain elusive 4,5. Here, to address this need, we developed a workflow that generates detailed quantitative maps of genetic subclone composition across whole-tumour sections. These provide the basis for studying clonal growth patterns, and the histological characteristics, microanatomy and microenvironmental composition of each clone. The approach rests on whole-genome sequencing, followed by highly multiplexed base-specific in situ sequencing, single-cell resolved transcriptomics and dedicated algorithms to link these layers. Applying the base-specific in situ sequencing workflow to eight tissue sections from two multifocal primary breast cancers revealed intricate subclonal growth patterns that were validated by microdissection. In a case of ductal carcinoma in situ, polyclonal neoplastic expansions occurred at the macroscopic scale but segregated within microanatomical structures. Across the stages of ductal carcinoma in situ, invasive cancer and lymph node metastasis, subclone territories are shown to exhibit distinct transcriptional and histological features and cellular microenvironments. These results provide examples of the benefits afforded by spatial genomics for deciphering the mechanisms underlying cancer evolution and microenvironmental ecology.
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
Nowell, P. C. (1976) · Science · doi:10.1126/science.959840 · Cited by 6,471
Nothing in Biology Makes Sense except in the Light of Evolution
Dobzhansky, T. (1973) · The American Biology Teacher · doi:10.2307/4444260 · Cited by 3,219
Greaves, M., & Maley, C. C. (2012) · Nature · doi:10.1038/nature10762 · Cited by 3,162
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
Rodriques, S. G., Stickels, R. R., Goeva, A., Martin, C. A., Murray, E., Vanderburg, C. R., Welch, J., Chen, L. M., Chen, F., & Macosko, E. Z. (2019) · Science · doi:10.1126/science.aaw1219 · Cited by 2,424
Tracking the Evolution of Non–Small-Cell Lung Cancer
Jamal-Hanjani, M., Wilson, G. A., McGranahan, N., Birkbak, N. J., Watkins, T. B. K., Veeriah, S., Shafi, S., Johnson, D. H., Mitter, R., Rosenthal, R., et al. (2017) · New England Journal of Medicine · doi:10.1056/nejmoa1616288 · Cited by 2,349
Self-citationTranscriptome-scale super-resolved imaging in tissues by RNA seqFISH
Eng, C.-H. L., Lawson, M., Zhu, Q., Dries, R., Koulena, N., Takei, Y., Yun, J., Cronin, C., Karp, C., Yuan, G.-C., et al. (2019) · Nature · doi:10.1038/s41586-019-1049-y · Cited by 1,754
The Life History of 21 Breast Cancers
Nik-Zainal, S., Van Loo, P., Wedge, D. C., Alexandrov, L. B., Greenman, C. D., Lau, K. W., Raine, K., Jones, D., Marshall, J., Ramakrishna, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.023 · Cited by 1,443
Self-citationIn situ sequencing for RNA analysis in preserved tissue and cells
Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wählby, C., & Nilsson, M. (2013) · Nature Methods · doi:10.1038/nmeth.2563 · Cited by 934
Self-citationClinical relevance of host immunity in breast cancer: from TILs to the clinic
Savas, P., Salgado, R., Denkert, C., Sotiriou, C., Darcy, P. K., Smyth, M. J., & Loi, S. (2016) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2015.215 · Cited by 890
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma
Bolli, N., Avet-Loiseau, H., Wedge, D. C., Van Loo, P., Alexandrov, L. B., Martincorena, I., Dawson, K. J., Iorio, F., Nik-Zainal, S., Bignell, G. R., et al. (2014) · Nature Communications · doi:10.1038/ncomms3997 · Cited by 875
Self-citation
Cited by
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics
Russell, A. J. C., Weir, J. A., Nadaf, N. M., Shabet, M., Kumar, V., Kambhampati, S., Raichur, R., Marrero, G. J., Liu, S., Balderrama, K. S., et al. (2024) · Nature · doi:10.1038/s41586-023-06837-4 · Cited by 225
OpenDVP: an experimental and computational framework for community-empowered deep visual proteomics
Nimo, J., Fritzsche, S., Valdes, D. S., Trinh, M., Pentimalli, T., Klingeberg, M., Schallenberg, S., Klauschen, F., Herse, F., Florian, S., et al. (2026) · Nature Methods · doi:10.1038/s41592-026-03262-z
Metadata
- Authors
- Lomakin, A., Svedlund, J., Strell, C., Gataric, M., Shmatko, A., Rukhovich, G., Park, J. S., Ju, Y. S., Dentro, S., Kleshchevnikov, V., Vaskivskyi, V., Li, T., Bayraktar, O. A., Pinder, S., Richardson, A. L., Santagata, S., Campbell, P. J., Russnes, H., Gerstung, M., Nilsson, M., & Yates, L. R.
- Venue
- Nature
- Published
- 2022-11-09
- Volume
- 611
- Issue
- 7936
- Pages
- 594-602
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W4308620811
- Cited by
- 181
- References
- 13
- FWCI
- 12.30
- 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: Spatial genomics maps the structure, nature and evolution of cancer clones. https://app.cochat.ai/papers/10.1038/s41586-022-05425-2
- The paper
- Lomakin, A., Svedlund, J., Strell, C., Gataric, M., Shmatko, A., Rukhovich, G., Park, J. S., Ju, Y. S., Dentro, S., Kleshchevnikov, V., Vaskivskyi, V., Li, T., Bayraktar, O. A., Pinder, S., Richardson, A. L., Santagata, S., Campbell, P. J., Russnes, H., Gerstung, M., . . . Yates, L. R. (2022). Spatial genomics maps the structure, nature and evolution of cancer clones. Nature. https://doi.org/10.1038/s41586-022-05425-2
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.
