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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
...lineage inference by allowing the examination of intratumor heterogeneity at cellular resolution. However, because single-cell sequencing data are derived from a limited amount of genetic material, the signals obtained are scarcer than those from bulk sequencing (Lähnemann et al. 2020). Genomic events...
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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
...that deviate slightly from the ISA from single-cell and bulk-sequencing data. However, these phylogeny approaches (other than OncoNEM) do not provide straightforward reconstruction of the tumor subclones. At the same time, none of these phylogeny-based methods account for cell doublets as the merged genotypes...

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