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Cited by 20

The DOI matches its Crossref record; 120 of the 120 references it cites were found in a registry or an index.

GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells

Turkalj, Sven, Jakobsen, Niels Asger, Groom, Angus, Metzner, Marlen, Riva, Simone G., Gür, E. Ravza, Usukhbayar, Batchimeg, Salazar, Mirian Angulo, Hentges, Lance D., Mickute, Gerda, Clark, Kevin, Sopp, Paul, Davies, James O.J., Hughes, Jim R., Vyas, Paresh·2023·Cell Stem Cell
DOI 10.1016/j.stem.2023.04.012
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Abstract

Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.

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Crossref · 10.1016/j.stem.2023.04.012

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Citations

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Research works printed but not linked: 3

  1. Rodriguez-Meira, 2022, Deciphering TP53 mutant cancer evolution with single-cell multi-omics, bioRxiv
  2. Woolley, 2021, INPP4B promotes leukemia by restricting leukemic stem cell differentiation through regulation of lysosomal functions, bioRxiv
  3. Myers, 2022, Integrated single-cell genotyping and chromatin accessibility charts JAK2 V617F human hematopoietic differentiation, bioRxiv

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Metadata

Authors
Turkalj, S., Jakobsen, N. A., Groom, A., Metzner, M., Riva, S. G., Gür, E. R., Usukhbayar, B., Salazar, M. A., Hentges, L. D., Mickute, G., Clark, K., Sopp, P., Davies, J. O. J., Hughes, J. R., & Vyas, P.
ORCID
Vyas, Paresh
Venue
Cell Stem Cell
Publisher
Elsevier BV
Published
2023-05
Volume
30
Issue
5
Pages
722-740.e11
ISSN
1934-5909
DOI
10.1016/j.stem.2023.04.012
Cited by
20
References
120
Language
en
Licence
Funders
  • Wellcome Trust (106130/Z/14/Z)
  • Clarendon Fund
  • Medical Research Council (MC_UU_00029/8, MR/R002258/1)
  • Blood Cancer UK (13008)
  • National Institute for Health and Care Research
  • Lister Institute of Preventive Medicine
  • Lady Tata Memorial Trust (MC_UU_00029/3)
  • National Institutes of Health (R24DK106766)
  • Kementerian Pendidikan Nasional

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CoChat. (2026). Citation check: GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. https://app.cochat.ai/papers/10.1016/j.stem.2023.04.012
The paper
Turkalj, S., Jakobsen, N. A., Groom, A., Metzner, M., Riva, S. G., Gür, E. R., Usukhbayar, B., Salazar, M. A., Hentges, L. D., Mickute, G., Clark, K., Sopp, P., Davies, J. O. J., Hughes, J. R., & Vyas, P. (2023). GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell. https://doi.org/10.1016/j.stem.2023.04.012

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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.