Searching journal content for articles similar to Leung et al..

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  1. 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...
  2. 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
    ...reconstruction error (Supplemental Fig. S27) was also smaller in all but one setting (n = 100 and 15% missing data).Inference of clonal clusters, genotypes, and phylogeny from experimental SCS dataWe applied SiCloneFit to two experimental single-cell DNA sequencing data sets from two metastatic colon cancer...
  3. 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
    ...of copies of a variant allele, this can even be potentially beneficial and reduce allelic dropout (since such an event would provide more starting material for the PCR amplification step that is typically performed prior to DNA sequencing).We ran PhISCS using single-cell data, first without considering any...
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  4. 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
    ...(cf. Fig. 2). The development of single-cell sequencing methods A typical cancer cell contains∼6–12 pg of DNA and 10–50 pg of total RNA (1%–5% mRNA), depending on the ploidy and the cell type (Livesey 2003). Therefore, the first step in any SCS experiment involves whole- amplification (WGA) or whole...
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  5. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ..., Sei E, Vilar E, Maru D, Kopetz S, Navin NE. 2017. Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer. Genome Res 27: 1287–1299. doi:10.1101/gr.209973.116 ↵McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S...
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