High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes
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Abstract
High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as antigen receptors. To overcome this limitation, we combined targeted capture and long-read sequencing of T-cell-receptor (TCR) and B-cell-receptor (BCR) mRNA transcripts with short-read transcriptome profiling of barcoded single-cell libraries generated by droplet-based partitioning. We show that Repertoire and Gene Expression by Sequencing (RAGE-Seq) can generate accurate full-length antigen receptor sequences at nucleotide resolution, infer B-cell clonal evolution and identify alternatively spliced BCR transcripts. We apply RAGE-Seq to 7138 cells sampled from the primary tumor and draining lymph node of a breast cancer patient to track transcriptome profiles of expanded lymphocyte clones across tissues. Our results demonstrate that RAGE-Seq is a powerful method for tracking the clonal evolution from large numbers of lymphocytes applicable to the study of immunity, autoimmunity and cancer.
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V(D)J regions of rearranged TCR/BCR mRNAs are located in the first ~500 nucleotides of the 5′ end of the transcripts.
“The V(D)J regions of rearranged TCR and BCR mRNAs are located in the first ~500 nucleotides of the 5′ end of the transcripts”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [90]
Several methods have been published pairing gene expression with TCR sequences in single cells.
“Several methods have been published pairing gene expression with TCR sequences in single cells89–92.”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [90]
Short-read scRNA-seq is not always sufficient to resolve genetic complexity of TCR/BCR isoforms while preserving accurate gene expression quantification at the 3′ end.
“short-read scRNA-seq is not always sufficient to resolve the genetic complexity of these isoforms while preserving accurate gene expression quantification at the 3′ end of the transcripts90.”
From The technological landscape and applications of single-cell multi-omics (2023) · cites this paper as [90]
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Nanopore sequencing technology, bioinformatics and applications
Wang, Y., Zhao, Y., Bollas, A. E., Wang, Y., & Au, K. F. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01108-x · Cited by 1,756 · see citing works
The technological landscape and applications of single-cell multi-omics
Baysoy, A., Bai, Z., Satija, R., & Fan, R. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00615-w · Cited by 1,037 · see citing works
Andersson, A., Larsson, L., Stenbeck, L., Salmén, F., Ehinger, A., Wu, S. Z., Al-Eryani, G., Roden, D., Swarbrick, A., Borg, Å., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26271-2 · Cited by 404 · see citing works
Self-citationMoragues, T., Mendoza, D. A., Beneyton, T., Modavi, C., Simutis, K., Abate, A. R., Baret, J., deMello, A. J., Densmore, D. M., & Griffiths, A. D. (2023) · Nature Reviews Methods Primers · doi:10.1038/s43586-023-00212-3 · Cited by 340 · see citing works
High-throughput and single-cell T cell receptor sequencing technologies
Pai, J. A., & Satpathy, A. T. (2021) · Nature Methods · doi:10.1038/s41592-021-01201-8 · Cited by 296 · see citing works
Unraveling B cell trajectories at single cell resolution
Morgan, D., & Tergaonkar, V. (2022) · Trends in Immunology · doi:10.1016/j.it.2022.01.003 · Cited by 232 · see citing works
High throughput error corrected Nanopore single cell transcriptome sequencing
Lebrigand, K., Magnone, V., Barbry, P., & Waldmann, R. (2020) · Nature Communications · doi:10.1038/s41467-020-17800-6 · Cited by 236 · see citing works
Tian, L., Jabbari, J. S., Thijssen, R., Gouil, Q. A., Amarasinghe, S. L., Voogd, O., Kariyawasam, H., Du, M. R. M., Schuster, J., Wang, C., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02525-6 · Cited by 207 · see citing works
The Great Immune Escape: Understanding the Divergent Immune Response in Breast Cancer Subtypes
Onkar, S., Carleton, N. M., Lucas, P. C., Bruno, T. C., Lee, A. V., Vignali, D. A. A., & Oesterreich, S. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0475 · Cited by 217 · see citing works
Pardo-Palacios, F. J., Arzalluz-Luque, Á., Kondratova, L., Salguero, P., Mestre‐Tomás, J., Amorín, R., Estevan-Morió, E., Liu, T., Nanni, A. V., McIntyre, L. M., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02229-2 · Cited by 208 · see citing works
Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE
You, Y., Prawer, Y. D. J., Paoli‐Iseppi, R. D., Hunt, C. P. J., Parish, C. L., Shim, H., & Clark, M. B. (2023) · Genome biology · doi:10.1186/s13059-023-02907-y · Cited by 179 · see citing works
Dysregulation and therapeutic targeting of RNA splicing in cancer
Stanley, R. F., & Abdel-Wahab, O. I. (2022) · Nature Cancer · doi:10.1038/s43018-022-00384-z · Cited by 160 · see citing works
Progress and Prospect of Immunotherapy for Triple-Negative Breast Cancer
Luo, C., Wang, P., He, S., Zhu, J., Shi, Y., & Wang, J. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.919072 · Cited by 147 · see citing works
Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics
Engblom, C., Thrane, K., Lin, Q., Andersson, A., Toosi, H., Chen, X., Steiner, E., Lu, C., Mantovani, G., Hagemann-Jensen, M., et al. (2023) · Science · doi:10.1126/science.adf8486 · Cited by 149 · see citing works
Recent advances in single-cell sequencing technologies
Wen, L., & Tang, F. (2022) · Precision Clinical Medicine · doi:10.1093/pcmedi/pbac002 · Cited by 127 · see citing works
Antibody display technologies: selecting the cream of the crop
Valldorf, B., Hinz, S. C., Russo, G., Pekar, L., Mohr, L., Klemm, J., Doerner, A., Krah, S., Hust, M., & Zielonka, S. (2021) · Biological Chemistry · doi:10.1515/hsz-2020-0377 · Cited by 130 · see citing works
TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
Tu, A. A., Gierahn, T. M., Monian, B., Morgan, D. M., Mehta, N. K., Ruiter, B., Shreffler, W. G., Shalek, A. K., & Love, J. C. (2019) · Nature Immunology · doi:10.1038/s41590-019-0544-5 · Cited by 128 · see citing works
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue
Hardwick, S. A., Hu, W., Joglekar, A., Fan, L., Collier, P. G., Foord, C., Balacco, J., Lanjewar, S., Sampson, M. M., Koopmans, F., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01231-3 · Cited by 119 · see citing works
Methodologies for Transcript Profiling Using Long-Read Technologies
Oikonomopoulos, S., Bayega, A., Fahiminiya, S., Djambazian, H. H. V., Bérubé, P., & Ragoussis, J. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00606 · Cited by 111 · see citing works
Joglekar, A., Hu, W., Zhang, B., Narykov, O., Diekhans, M., Marrocco, J., Balacco, J., Ndhlovu, L. C., Milner, T. A., Fedrigo, O. D., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01616-4 · Cited by 122 · see citing works
Transcriptomics in the era of long-read sequencing
Monzó, C., Liu, T.-Y., & Conesa, A. (2025) · Nature reviews genetics · doi:10.1038/s41576-025-00828-z · Cited by 110 · see citing works
A single-cell survey of cellular hierarchy in acute myeloid leukemia
Wu, J., Xiao, Y., Sun, J., Sun, H., Chen, H., Zhu, Y., Fu, H., Yu, C., Weigao, E., Lai, S., et al. (2020) · Journal of Hematology & Oncology · doi:10.1186/s13045-020-00941-y · Cited by 110 · see citing works
Droplet-based single cell RNAseq tools: a practical guide
Salomon, R., Kaczorowski, D., Valdes-Mora, F., Nordon, R. E., Neild, A., Farbehi, N., Bartonicek, N., & Gallego-Ortega, D. (2019) · Lab on a Chip · doi:10.1039/c8lc01239c · Cited by 109 · see citing works
Nanopore sequencing: flourishing in its teenage years
Zhang, T., Li, H., Jiang, M., Hou, H., Gao, Y., Li, Y., Wang, F., Wang, J., Peng, K., & Liu, Y. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.09.007 · Cited by 111 · see citing works
Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing
Fan, X., Tang, D., Liao, Y., Li, P., Zhang, Y., Wang, M., Liang, F., Wang, X., Gao, Y., Wen, L., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3001017 · Cited by 103 · see citing works
Harris, R. J. C., Cheung, A., Ng, J. C.-F., Laddach, R., Chenoweth, A. M., Crescioli, S., Fittall, M. W., Dominguez-Rodriguez, D., Roberts, J., Levi, D., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-20-3773 · Cited by 100 · see citing works
Single-cell isoform analysis in human immune cells
Volden, R., & Vollmers, C. (2022) · Genome biology · doi:10.1186/s13059-022-02615-z · Cited by 85 · see citing works
Single-cell immunology: Past, present, and future
Ginhoux, F., Yalin, A., Dutertre, C., & Amit, I. (2022) · Immunity · doi:10.1016/j.immuni.2022.02.006 · Cited by 93 · see citing works
JAFFAL: detecting fusion genes with long-read transcriptome sequencing
Davidson, N., Chen, Y., Sadras, T., Ryland, G. L., Blombery, P. A., Ekert, P. G., Göke, J., & Oshlack, A. (2022) · Genome biology · doi:10.1186/s13059-021-02588-5 · Cited by 86 · see citing works
Immunology Driven by Large-Scale Single-Cell Sequencing
Gomes, T., Teichmann, S. A., & Talavera-López, C. N. (2019) · Trends in Immunology · doi:10.1016/j.it.2019.09.004 · Cited by 71 · see citing works
Wu, C.-Y., Lau, B. T., Kim, H. S., Sathe, A., Grimes, S. M., Ji, H. P., & Zhang, N. R. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00911-w · Cited by 70 · see citing works
Updates on Immunotherapy and Immune Landscape in Renal Clear Cell Carcinoma
Kim, M., Jin, Z., Kolb, R. H., Borcherding, N. C., Chatzkel, J. A., Falzarano, S. M., & Zhang, W. (2021) · Cancers · doi:10.3390/cancers13225856 · Cited by 78 · see citing works
Computational immunogenomic approaches to predict response to cancer immunotherapies
Addala, V., Newell, F., Pearson, J. V., Redwood, A., Robinson, B. W. S., Creaney, J., & Waddell, N. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00830-6 · Cited by 77 · see citing works
Single-Cell Techniques and Deep Learning in Predicting Drug Response
Wu, Z., Lawrence, P. J., Ma, A., Zhu, J., Xu, D., & Ma, Q. (2020) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2020.10.004 · Cited by 68 · see citing works
Masle‐Farquhar, E., Jackson, K., Peters, T. J., Al‐Eryani, G., Singh, M., Payne, K. J., Rao, G., Avery, D. T., Apps, G., Kingham, J., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.11.001 · Cited by 68 · see citing works
Self-citationJiang, R., Fichtner, M. L., Hoehn, K. B., Pham, M. C., Stathopoulos, P., Nowak, R. J., Kleinstein, S. H., & O’Connor, K. C. (2020) · JCI Insight · doi:10.1172/jci.insight.136471 · Cited by 65 · see citing works
Recent advances in high-throughput single-cell transcriptomics and spatial transcriptomics
Shen, X., Zhao, Y., Wang, Z., & Shi, Q. (2022) · Lab on a Chip · doi:10.1039/d2lc00633b · Cited by 65 · see citing works
High-Throughput Routes to Biomaterials Discovery
Soheilmoghaddam, M., Rumble, M., & Cooper-White, J. J. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01026 · Cited by 65 · see citing works
Skin colonization by circulating neoplastic clones in cutaneous T-cell lymphoma
Iyer, A., Hennessey, D., O’Keefe, S. L., Patterson, J., Wang, W., Wong, G. K., & Gniadecki, R. (2019) · Blood · doi:10.1182/blood.2019002516 · Cited by 62 · see citing works
The current landscape of single-cell transcriptomics for cancer immunotherapy
Guruprasad, P., Lee, Y. G., Kim, K. H., & Ruella, M. (2020) · The Journal of Experimental Medicine · doi:10.1084/jem.20201574 · Cited by 63 · see citing works
Single-cell genomics in plants: current state, future directions, and hurdles to overcome
Cuperus, J. T. (2021) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiab478 · Cited by 61 · see citing works
Single‐Cell Sequencing Methodologies: From Transcriptome to Multi‐Dimensional Measurement
Chen, Y., Song, J. T., Ruan, Q., Zeng, X., Wu, L., Cai, L., Wang, X., & Yang, C. J. (2021) · Small Methods · doi:10.1002/smtd.202100111 · Cited by 59 · see citing works
Isoform Age - Splice Isoform Profiling Using Long-Read Technologies
Paoli‐Iseppi, R. D., Gleeson, J., & Clark, M. B. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.711733 · Cited by 59 · see citing works
Vries, N. L. D., Mahfouz, A. E., Koning, F., & de Miranda, N. F. C. C. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.01254 · Cited by 58 · see citing works
Hu, X., Yang, P., Chen, S., Wei, G., Yuan, L., Yang, Z., Gong, L., He, L., Yang, L., Peng, S., et al. (2023) · Breast Cancer Research · doi:10.1186/s13058-023-01639-y · Cited by 61 · see citing works
The Application of Single‐Cell RNA Sequencing in Vaccinology
Noé, A., Cargill, T. N., Nielsen, C. M., Russell, A. J. C., & Barnes, E. J. (2020) · Journal of Immunology Research · doi:10.1155/2020/8624963 · Cited by 58 · see citing works
Adaptive immune receptor repertoire analysis
Mhanna, V., Bashour, H., Quý, K. L., Barennes, P., Rawat, P., Greiff, V., & Mariotti‐Ferrandiz, E. (2024) · Nature Reviews Methods Primers · doi:10.1038/s43586-023-00284-1 · Cited by 62 · see citing works
Kim, H. S., Kweon, J., & Kim, Y. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01212-3 · Cited by 64 · see citing works
DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Zhou, Z., Xu, B., Minn, A. J., & Zhang, N. R. (2020) · Genome biology · doi:10.1186/s13059-019-1922-x · Cited by 56 · see citing works
ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms
Sheynkman, G., Tuttle, K. S., Laval, F., Tseng, E., Underwood, J. G., Yu, L., Dong, D., Smith, M. L., Sebra, R., Willems, L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16174-z · Cited by 55 · see citing works
Self-citationValkiers, S., de Vrij, N., Gielis, S., Verbandt, S., Ogunjimi, B., Laukens, K., & Meysman, P. (2022) · ImmunoInformatics · doi:10.1016/j.immuno.2022.100009 · Cited by 52 · see citing works
High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq
Benotmane, J. K., Kueckelhaus, J., Will, P., Zhang, J., Ravi, V. M., Joseph, K., Sankowski, R., Beck, J., Lee-Chang, C., Schnell, O., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43201-6 · Cited by 59 · see citing works
Hegenbarth, J.-C., Lezzoche, G., Windt, L. J. D., & Stoll, M. (2022) · Frontiers in Molecular Medicine · doi:10.3389/fmmed.2022.839338 · Cited by 56 · see citing works
Single-cell RNA-seq methods to interrogate virus-host interactions
Ratnasiri, K., Wilk, A. J., Lee, M. J., Khatri, P., & Blish, C. A. (2022) · Seminars in Immunopathology · doi:10.1007/s00281-022-00972-2 · Cited by 53 · see citing works
RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
de la Rubia, I., Srivastava, A., Xue, W., Indi, J. A., Sala, S. C., Lagarde, J., Albà, M. M., & Eyras, E. (2022) · Genome biology · doi:10.1186/s13059-022-02715-w · Cited by 50 · see citing works
Li, B., Pei, G., Yao, J., Ding, Q., Jia, P., & Zhao, Z. (2021) · Oncogene · doi:10.1038/s41388-021-01870-x · Cited by 48 · see citing works
Advances in single-cell long-read sequencing technologies
Gupta, P., O’Neill, H., Wolvetang, E. J., Chatterjee, A., & Gupta, I. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae047 · Cited by 49 · see citing works
Yermanos, A., Agrafiotis, A., Kuhn, R., Robbiani, D., Yates, J., Papadopoulou, C., Han, J., Sandu, I., Weber, C. R., Bieberich, F., et al. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab023 · Cited by 45 · see citing works
Zeng, L., Yang, K., Zhang, T., Zhu, X., Hao, W., Chen, H., & Ge, J. (2022) · Journal of Autoimmunity · doi:10.1016/j.jaut.2022.102919 · Cited by 45 · see citing works
Diversity in recognition and function of human γδ T cells
Castro, C. D., Boughter, C. T., Broughton, A. E., Ramesh, A., & Adams, E. J. (2020) · Immunological Reviews · doi:10.1111/imr.12930 · Cited by 44 · see citing works
Preneoplastic somatic mutations including MYD88 L265P in lymphoplasmacytic lymphoma
Rodríguez, S., Celay, J., Goicoechea, I., Jiménez, C., Botta, C., Garcia-Barchino, M. J., Garcés, J., Larráyoz, M., Santos, S. A., Alignani, D., et al. (2022) · Science Advances · doi:10.1126/sciadv.abl4644 · Cited by 43 · see citing works
Pokhilko, A. V., Handel, A. E., Curion, F., Volpato, V., Whiteley, E. S., Bøstrand, S. M. K., Newey, S. E., Akerman, C. J., Webber, C., Clark, M. B., et al. (2021) · Genome Research · doi:10.1101/gr.273961.120 · Cited by 43 · see citing works
Challenges and Opportunities in the Clinical Translation of High-Resolution Spatial Transcriptomics
Pentimalli, T. M., Karaiskos, N., & Rajewsky, N. (2024) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-111523-023417 · Cited by 44 · see citing works
Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
Byrne, A., Le, D., Sereti, K., Menon, H., Vaidya, S., Patel, N., Lund, J. M., Xavier‐Magalhães, A., Shi, M., Liang, Y., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51252-6 · Cited by 42 · see citing works
Genome annotation: From human genetics to biodiversity genomics
Guigó, R. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100375 · Cited by 41 · see citing works
Zhang, Z., Bae, B., Dredge, W. H., & Miura, P. (2023) · Nature Communications · doi:10.1038/s41467-023-41207-8 · Cited by 40 · see citing works
Mikheenko, A., Prjibelski, A. D., Joglekar, A., & Tilgner, H. (2022) · Genome Research · doi:10.1101/gr.276405.121 · Cited by 40 · see citing works
BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data
Boggy, G. J., McElfresh, G., Mahyari, E., Ventura, A. B., Hansen, S. G., Picker, L. J., & Bimber, B. N. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac213 · Cited by 38 · see citing works
Louie, R., Cai, C., Samir, J., Singh, M., Deveson, I. W., Ferguson, J. M., Amos, T., McGuire, H., Gowrishankar, K., Adikari, T., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43656-7 · Cited by 36 · see citing works
Self-citationAdvances in long-read single-cell transcriptomics
Kumari, P., Kaur, M., Dindhoria, K., Ashford, B., Amarasinghe, S. L., & Thind, A. S. (2024) · Human Genetics · doi:10.1007/s00439-024-02678-x · Cited by 37 · see citing works
Long-read sequencing to understand genome biology and cell function
Kraft, F., & Kurth, I. (2020) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2020.105799 · Cited by 37 · see citing works
Delyon, J., Zuber, J., Dorent, R., Poujol‐Robert, A., Péraldi, M., Anglicheau, D., & Lebbé, C. (2020) · Transplantation · doi:10.1097/tp.0000000000003292 · Cited by 34 · see citing works
Liu, Q., Wang, Z., Jiang, Y., Shao, F., Ma, Y., Zhu, M., Luo, Q., Bi, Y., Cao, L., Peng, L., et al. (2022) · Genes & Diseases · doi:10.1016/j.gendis.2021.12.020 · Cited by 34 · see citing works
Methods for sequence and structural analysis of B and T cell receptor repertoires
Teraguchi, S., Saputri, D. S., Llamas-Covarrubias, M. A., Davila, A., Díez, D., Nazlica, S. A., Rozewicki, J., Ismanto, H. S., Wilamowski, J., Xie, J., et al. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.07.008 · Cited by 33 · see citing works
Chowdhury, T., Cressiot, B., Parisi, C., Smolyakov, G., Thiébot, B., Trichet, L., Fernandes, F. M., Pelta, J., & Manivet, P. (2023) · ACS Sensors · doi:10.1021/acssensors.2c02308 · Cited by 33 · see citing works
Leveraging the power of long reads for targeted sequencingPreprint
Iyer, S. V., Goodwin, S., & McCombie, W. R. (2024) · Genome Research · doi:10.1101/gr.279168.124 · Cited by 34 · see citing works
Castaldi, P. J., Abood, A., Farber, C. R., & Sheynkman, G. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac196 · Cited by 30 · see citing works
Milpied, P., Gandhi, A. K., Cartron, G., Pasqualucci, L., Tarte, K., Nadel, B., & Roulland, S. (2021) · Advances in immunology · doi:10.1016/bs.ai.2021.05.002 · Cited by 28 · see citing works
Heterogeneity of germinal center B cells: New insights from single‐cell studies
Attaf, N., Baaklini, S., Binet, L., & Milpied, P. (2021) · European Journal of Immunology · doi:10.1002/eji.202149235 · Cited by 31 · see citing works
Progress in Plant Genome Sequencing
Henry, R. J. (2022) · Applied Biosciences · doi:10.3390/applbiosci1020008 · Cited by 31 · see citing works
Application of third-generation sequencing in cancer research
Chen, Z., & He, X. (2021) · Medical Review · doi:10.1515/mr-2021-0013 · Cited by 30 · see citing works
Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination
Wu, S., & Schmitz, U. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.03.023 · Cited by 30 · see citing works
Spatial transcriptomics: a new frontier in cancer research
Huang, S., Ouyang, L., Tang, J., Qian, K., Chen, X., Xu, Z., Ming, J., & Xi, R. (2024) · Clinical Cancer Bulletin · doi:10.1007/s44272-024-00018-8 · Cited by 32 · see citing works
Understanding virus–host interactions in tissues
Speranza, E. E. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01434-7 · Cited by 29 · see citing works
Alternative splicing signatures in preimplantation embryo development
Tian, G. G., Li, J., & Wu, J. (2020) · Cell & Bioscience · doi:10.1186/s13578-020-00399-y · Cited by 29 · see citing works
Lyu, M., Wang, S., Gao, K., Wang, L., Zhu, X., Liu, Y., Wang, M., Liu, X., Li, B., & Tian, L. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.779961 · Cited by 28 · see citing works
Quantifying transcriptome diversity: a review
Jones, E. F., Haldar, A., Oza, V. H., & Lasseigne, B. N. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad019 · Cited by 27 · see citing works
Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples
Curion, F., Handel, A. E., Attar, M., Gallone, G., Bowden, R. J., Cader, M. Z., & Clark, M. B. (2020) · RNA Biology · doi:10.1080/15476286.2020.1777768 · Cited by 29 · see citing works
Rapid Identification and Evaluation of Neoantigen-reactive T-Cell Receptors From Single Cells
Paria, B. C., Levin, N., Lowery, F. J., Pasetto, A., Deniger, D. C., Parkhurst, M. R., Yossef, R., Kim, S. P., Florentin, M., Ngo, L. T., et al. (2020) · Journal of Immunotherapy · doi:10.1097/cji.0000000000000342 · Cited by 26 · see citing works
Arora, J. K., Opasawatchai, A., Poonpanichakul, T., Jiravejchakul, N., Sungnak, W., Sakuntabhai, A., Singhasivanon, P., Suraamornkul, S., Yingtaweesak, T., Manopwisedjaroen, K., et al. (2022) · iScience · doi:10.1016/j.isci.2022.104034 · Cited by 26 · see citing works
Big data-driven precision medicine: Starting the custom-made era of iatrology
Song, C. M., Kong, Y., Huang, L., Luo, H., & Zhu, X. M. (2020) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2020.110445 · Cited by 26 · see citing works
Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing
Yuan, C. U., Quah, F. X., & Hemberg, M. (2024) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2024.101255 · Cited by 25 · see citing works
Revealing the heterogeneity of CD4+ T cells through single-cell transcriptomics
Morgan, D. M., Shreffler, W. G., & Love, J. C. (2022) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2022.08.010 · Cited by 25 · see citing works
Belchikov, N., Hsu, J., Li, X. J., Jarroux, J., Hu, W., Joglekar, A., & Tilgner, H. (2024) · Genome Research · doi:10.1101/gr.279640.124 · Cited by 25 · see citing works
Applications of single-cell technologies in drug discovery for tumor treatment
Liu, B., Hu, S., & Wang, X. (2024) · iScience · doi:10.1016/j.isci.2024.110486 · Cited by 24 · see citing works
Young, C., Singh, M., Jackson, K., Field, M. A., Peters, T. J., Angioletti‐Uberti, S., Frenkel, D., Ravishankar, S., Gupta, M., Wang, J. J., et al. (2025) · Immunity · doi:10.1016/j.immuni.2024.12.011 · Cited by 24 · see citing works
Self-citationSingle-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations
Wang, M., Gu, M., Liu, L., Liu, Y., & Tian, L. (2021) · Vascular Health and Risk Management · doi:10.2147/vhrm.s288090 · Cited by 24 · see citing works
Ebrahimi, G., Orabi, B., Robinson, M., Chauve, C., Flannigan, R. K., & Hach, F. (2022) · iScience · doi:10.1016/j.isci.2022.104530 · Cited by 22 · see citing works
Practical Considerations for Single‐Cell Genomics
Regan, C., & Preall, J. B. (2022) · Current Protocols · doi:10.1002/cpz1.498 · Cited by 25 · see citing works
A current and future perspective on T cell receptor repertoire profiling
Shen, Y., Voigt, A., Leng, X., Rodriguez, A. A., & Nguyen, C. Q. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1159109 · Cited by 23 · see citing works
- Authors
- Singh, M., Al-Eryani, G., Carswell, S., Ferguson, J. M., Blackburn, J., Barton, K., Roden, D., Luciani, F., Giang Phan, T., Junankar, S., Jackson, K., Goodnow, C. C., Smith, M. A., & Swarbrick, A.
- Affiliations
- Garvan Institute of Medical Research (AU)
- UNSW Sydney (AU)
- Corresponding author
- Goodnow, Christopher C.
- Smith, Martin A.
- Swarbrick, Alexander
- ORCID
- Venue
- Nature Communications
- Published
- 2019-07-16
- Volume
- 10
- Issue
- 1
- Pages
- 3120-3120
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6635368
- OpenAlex
- W2958475422
- Cited by
- 308
- References
- 82
- Citations by year
- 2026: 22 · 2025: 30 · 2024: 46 · 2023: 50 · 2022: 60 · 2021: 46 · 2020: 46 · 2019: 7
- FWCI
- 13.73
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Department of Health | National Health and Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- single-cell RNA sequencing, T cell receptor, B cell receptor, antigen receptor repertoire, alternative splicing, breast cancer, tumor-draining lymph nodes, clonal tracking
- MeSH terms
- Humans, Lymphocytes, Receptors, Antigen, B-Cell, Receptors, Antigen, T-Cell, Sequence Analysis, RNA, Gene Expression Profiling, Single-Cell Analysis, High-Throughput Nucleotide Sequencing, Clonal Evolution, Primary Cell Culture
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