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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...), including HER2-driven breast cancer and BRAF-driven melanoma and colorectal cell lines.The SPLINTR (single-cell profiling and lineage tracing) approach was recently employed to investigate nonheritable genetic determinants in clonal dynamics within AML, in which the oncogenic fusions of the MLL1 gene...
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Method: Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data
- Liting Zhang,
- Hank W. Bass,
- Jerome Irianto,
- and Xian Mallory
Genome Res. November 2023 33: 2002-2017; Published in Advance November 22, 2023, doi:10.1101/gr.277249.122
..., Tallahassee, Florida 32306, USA Corresponding author: xfan2@fsu.eduAbstractSingle-cell DNA sequencing enables the construction of evolutionary trees that can reveal how tumors gain mutations and grow. Different whole- amplification procedures render genomic materials of different characteristics, often...
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Method: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
- Fei Qin,
- Guoshuai Cai,
- Christopher I. Amos,
- and Feifei Xiao
Genome Res. January 2024 34: 85-93; Published in Advance January 30, 2024, doi:10.1101/gr.278098.123
...studies characterize clonal diversity using bulk DNA sequencing (Oesper et al. 2013; Ha et al. 2014; Li and Li 2014; Zhang et al. 2014; Deshwar et al. 2015), which is limited to reporting only an average signal from complex populations of cells (Navin 2015). Single-cell sequencing (SCS) technology enables...
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Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
- Yuelin Liu,
- Xuan Cindy Li,
- Farid Rashidi Mehrabadi,
- Alejandro A. Schäffer,
- Drew Pratt,
- David R. Crawford,
- Salem Malikić,
- Erin K. Molloy,
- Vishaka Gopalan,
- Stephen M. Mount,
- Eytan Ruppin,
- Kenneth D. Aldape,
- and S. Cenk Sahinalp
Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
.... 2021). Because of the high level of sparsity in the mutation calls, we clustered single cells before constructing the mutation tree. We observed a high level of heterogeneity in terms of lesion of origin and sampling locations in the cell clusters (Supplemental Fig. S18), which makes inferring simple...
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Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
- Hamim Zafar,
- Nicholas Navin,
- Ken Chen,
- and Luay Nakhleh
Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
...). Another problem with SCS data is missing entries due to coverage nonuniformity (Zafar et al. 2018).Single-cell somatic point mutation profiles have been used to infer clonal subpopulations. Early studies (Li et al. 2012; Wang et al. 2014) used multidimensional scaling and hierarchical clustering...
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Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
- Salem Malikic,
- Farid Rashidi Mehrabadi,
- Simone Ciccolella,
- Md. Khaledur Rahman,
- Camir Ricketts,
- Ehsan Haghshenas,
- Daniel Seidman,
- Faraz Hach,
- Iman Hajirasouliha,
- and S. Cenk Sahinalp
Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
...that are sensitive to the noise characteristics of SCS data, while incorporating the assumptions of the clonal theory of cancer evolution to tumor evolution modeling.We note that a final additional source of noise is doublets, two (or rarely more) cells with heterogeneous mutation profiles treated as a single cell...
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Method: Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors
- Jack Kuipers,
- Katharina Jahn,
- Benjamin J. Raphael,
- and Niko Beerenwinkel
Genome Res. November 2017 27: 1885-1894; Published in Advance October 13, 2017, doi:10.1101/gr.220707.117
...is likely to be observed in practice. For bulk studies of admixed samples of cell, violations of the ISA may be obscured since mutational profiles are amalgamated before sequencing. Theymay therefore be challenging to detect when deconvolving the sample and reconstructing the tumor phylogeny. Single-cell...
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Research: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
- Marco L. Leung,
- Alexander Davis,
- Ruli Gao,
- Anna Casasent,
- Yong Wang,
- Emi Sei,
- Eduardo Vilar,
- Dipen Maru,
- Scott Kopetz,
- and Nicholas E. Navin
Genome Res. August 2017 27: 1287-1299; Published in Advance May 25, 2017, doi:10.1101/gr.209973.116
...intra-tumor heterogeneity at the primary and metastatic tumor sites. To address this problem, we developed a highly multiplexed single-cell DNA sequencing approach to trace the metastatic lineages of two CRC patients with matched liver metastases. Single-cell copy number or mutational profiling...
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Research: Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
- Lili Wang,
- Jean Fan,
- Joshua M. Francis,
- George Georghiou,
- Sarah Hergert,
- Shuqiang Li,
- Rutendo Gambe,
- Chensheng W. Zhou,
- Chunxiao Yang,
- Sheng Xiao,
- Paola Dal Cin,
- Michaela Bowden,
- Dylan Kotliar,
- Sachet A. Shukla,
- Jennifer R. Brown,
- Donna Neuberg,
- Dario R. Alessi,
- Cheng-Zhong Zhang,
- Peter V. Kharchenko,
- Kenneth J. Livak,
- and Catherine J. Wu
Genome Res. August 2017 27: 1300-1311; Published in Advance July 5, 2017, doi:10.1101/gr.217331.116
...branches, thus creating a cohesive expression profile in each CLL sample despite the presence of genetic heterogeneity. Our study highlights the potential for single-cell RNA-based targeted analysis to sensitively determine transcriptional and mutational profiles of individual cancer cells, leading...
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Perspective: The first five years of single-cell cancer genomics and beyond
- Nicholas E. Navin
Genome Res. October 2015 25: 1499-1507; doi:10.1101/gr.191098.115
.... (2015) 25858951 Multiplexed single-cell copy number profiling to study clonal diversity in breast tumors Xenografts Breast xenografts DNA-SCS Eirew et al. (2014) 25470049 Clonal dynamics and evolution in xenografts Cell lines Colon DNA-SCS Zong et al. (2012) 23258894 Mutation rates in a colon cancer...
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