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Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

https://doi.org/10.1101/411058
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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A Conditional Mouse Model of Synovial Sarcoma: Insights into a Myogenic Origin
inferredcites →https://doi.org/10.1016/j.cell.2012.02.028openalex-snapshot
Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm
inferredcites →https://doi.org/10.1016/j.cell.2015.05.002openalex-snapshot
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
inferredcites →https://doi.org/10.1016/j.cell.2018.07.042openalex-snapshot
Chromosome Segregation Fidelity in Epithelia Requires Tissue Architecture
inferredcites →https://doi.org/10.1016/j.celrep.2017.05.055openalex-snapshot
p53 Prohibits Propagation of Chromosome Segregation Errors that Produce Structural Aneuploidies
inferredcites →https://doi.org/10.1016/j.molcel.2017.01.023openalex-snapshot
Comparative Analysis of Single-Cell RNA Sequencing Methods
inferredcites →https://doi.org/10.1038/nature04226openalex-snapshot
A haplotype map of the human genome
inferredcites →https://doi.org/10.1038/nature09807openalex-snapshot
Tumour evolution inferred by single-cell sequencing
inferredcites →https://doi.org/10.1038/nature13600openalex-snapshot
Clonal evolution in breast cancer revealed by single nucleus genome sequencing
inferredcites →https://doi.org/10.1038/nature13952openalex-snapshot
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution
inferredcites →https://doi.org/10.1038/nbt.2892openalex-snapshot
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
inferredcites →https://doi.org/10.1038/ng.3573openalex-snapshot
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
inferredcites →https://doi.org/10.1038/nmeth.1785openalex-snapshot
A linear complexity phasing method for thousands of genomes
inferredcites →https://doi.org/10.1038/nmeth.4140openalex-snapshot
Scalable whole-genome single-cell library preparation without preamplification
inferredcites →https://doi.org/10.1038/nmeth.4154openalex-snapshot
Sequencing thousands of single-cell genomes with combinatorial indexing
inferredcites →https://doi.org/10.1038/nmeth.4303openalex-snapshot
E-scape: interactive visualization of single-cell phylogenetics and cancer evolution
inferredcites →https://doi.org/10.1038/nprot.2012.039openalex-snapshot
Genome-wide copy number analysis of single cells
inferredcites →https://doi.org/10.1038/nprot.2017.029openalex-snapshot
Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs
inferredcites →https://doi.org/10.1038/nrg.2015.16openalex-snapshot
Single-cell genome sequencing: current state of the science
inferredcites →https://doi.org/10.1038/s41467-017-00244-wopenalex-snapshot
Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer
inferredcites →https://doi.org/10.1073/pnas.0912402107openalex-snapshot
Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
inferredcites →https://doi.org/10.1073/pnas.1320659110openalex-snapshot
Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients
inferredcites →https://doi.org/10.1073/pnas.1415287111openalex-snapshot
Single cell sequencing reveals low levels of aneuploidy across mammalian tissues
inferredcites →https://doi.org/10.1073/pnas.1420822111openalex-snapshot
Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics
inferredcites →https://doi.org/10.1073/pnas.1520964113openalex-snapshot
Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
inferredcites →https://doi.org/10.1093/bioinformatics/btr629openalex-snapshot
Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bts271openalex-snapshot
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
inferredcites →https://doi.org/10.1093/hmg/ddh016openalex-snapshot
Replication timing of the human genome
inferredcites →https://doi.org/10.1093/nar/gks001openalex-snapshot
Summarizing and correcting the GC content bias in high-throughput sequencing
inferredcites →https://doi.org/10.1101/117523openalex-snapshot
deStruct: Accurate Rearrangement Detection using Breakpoint Specific Realignment
inferredcites →https://doi.org/10.1101/gr.137570.112openalex-snapshot
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
inferredcites →https://doi.org/10.1101/gr.180281.114openalex-snapshot
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
inferredcites →https://doi.org/10.1126/science.1229164openalex-snapshot
Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell
inferredcites →https://doi.org/10.1186/1471-2407-12-379openalex-snapshot
Derivation and characterization of matched cell lines from primary and recurrent serous ovarian cancer
inferredcites →https://doi.org/10.1186/s12864-017-3893-1openalex-snapshot
Massively parallel nanowell-based single-cell gene expression profiling
inferredcites →https://doi.org/10.1186/s13058-014-0510-yopenalex-snapshot
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation
inferredcites →https://doi.org/10.1186/s13059-017-1267-2openalex-snapshot
ReMixT: clone-specific genomic structure estimation in cancer
inferredcites →https://doi.org/10.1186/s13742-015-0091-4openalex-snapshot
Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells
inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection
inferredcites →https://doi.org/10.48550/arxiv.1802.03426openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← backgroundhttps://doi.org/10.5281/zenodo.5725635zenodo-depositor-declared
inferred← citeshttps://doi.org/10.1016/j.cels.2020.03.005openalex-snapshot
SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing
inferred← citeshttps://doi.org/10.1038/s41576-019-0114-6openalex-snapshot
Resolving genetic heterogeneity in cancer
inferred← citeshttps://doi.org/10.1101/533323openalex-snapshot
Multi-omic analysis of CIC’s functional networks reveals novel interaction partners and a potential role in mitotic fidelity
inferred← citeshttps://doi.org/10.1101/696179openalex-snapshot
Methods for Copy Number Aberration Detection from Single-cell DNA Sequencing Data
inferred← citeshttps://doi.org/10.1101/gr.278098.123openalex-snapshot
A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
inferred← citeshttps://doi.org/10.1186/s13059-019-1645-zopenalex-snapshot
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
inferred← citeshttps://doi.org/10.1186/s13059-020-02119-8openalex-snapshot
Methods for copy number aberration detection from single-cell DNA-sequencing data
inferred← citeshttps://doi.org/10.1186/s13059-020-1926-6openalex-snapshot
Eleven grand challenges in single-cell data science
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006832openalex-snapshot
Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008012openalex-snapshot
Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data
inferred← citeshttps://doi.org/10.3390/cancers11020226openalex-snapshot
Detecting Chromosome Instability in Cancer: Approaches to Resolve Cell-to-Cell Heterogeneity
inferred← citeshttps://doi.org/10.3390/ijms23031861openalex-snapshot
Theranostic Interpolation of Genomic Instability in Breast Cancer
inferred← citeshttps://doi.org/10.7554/elife.55207openalex-snapshot
A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes
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