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
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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“Therefore, it is universal in single-cell genotyping to observe a distribution of scVAFs that will range from ∼1% (0.01) to ∼99% (0.99).59,99,112”
From Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging (2024) · cites this paper as [99]
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Cites
The Sequence Alignment/Map format and SAMtools
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Integrated analysis of multimodal single-cell data
Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W. M., Zheng, S., Butler, A., Lee, M. J., Wilk, A. J., Darby, C., Zagar, M., et al. (2020) · doi:10.1101/2020.10.12.335331 · Cited by 15,508
Tissue-based map of the human proteome
Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., & Madden, T. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-134 · Cited by 6,507
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
The Cancer Genome Atlas Research Network (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1301689 · Cited by 5,078
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
Cibulskis, K., Lawrence, M. S., Carter, S. L., Sivachenko, A., Jaffe, D. B., Sougnez, C. L., Gabriel, S., Meyerson, M. M., Lander, E. S., & Getz, G. A. (2013) · Nature Biotechnology · doi:10.1038/nbt.2514 · Cited by 5,013
COSMIC: the Catalogue Of Somatic Mutations In Cancer
Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., Bindal, N., Boutselakis, H., Cole, C. G., Creatore, C., Dawson, E., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1015 · Cited by 4,867
Age-related clonal hematopoiesis associated with adverse outcomes
Jaiswal, S., Fontanillas, P., Flannick, J., Manning, A., Grauman, P. V., Mar, B. G., Lindsley, R. C., Mermel, C. H., Burtt, N., Chavez, A., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1408617 · Cited by 4,841
Genomic classification and prognosis in acute myeloid leukemia
Papaemmanuil, E., Gerstung, M., Bullinger, L., Gaidzik, V. I., Paschka, P., Roberts, N. D., Potter, N. E., Heuser, M., Thol, F., Bolli, N., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1516192 · Cited by 4,350
Research works printed but not linked: 3
- Rodriguez-Meira, 2022, Deciphering TP53 mutant cancer evolution with single-cell multi-omics, bioRxiv
- Woolley, 2021, INPP4B promotes leukemia by restricting leukemic stem cell differentiation through regulation of lysosomal functions, bioRxiv
- Myers, 2022, Integrated single-cell genotyping and chromatin accessibility charts JAK2 V617F human hematopoietic differentiation, bioRxiv
Cited by
Jakobsen, N. A., Turkalj, S., Zeng, A. G. X., Stoilova, B., Metzner, M., Rahmig, S., Nagree, M. S., Shah, S., Moore, R., Usukhbayar, B., et al. (2024) · Cell Stem Cell · doi:10.1016/j.stem.2024.05.010 · Cited by 130
Self-citation
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
- Cited by
- 20
- References
- 120
- Language
- en
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 369 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- 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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