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Retrospective cell lineage reconstruction in Humans using short tandem repeats

https://doi.org/10.1101/191296

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What this work says

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

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Rapid Multiplexed Genotyping of Simple Tandem Repeats using Capture and High-Throughput Sequencing

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Concise Review: Age-Related Clonal Hematopoiesis: Stem Cells Tempting the Devil

inferredcites →https://doi.org/10.1016/0012-1606(77)90158-0openalex-snapshot

Post-embryonic cell lineages of the nematode, Caenorhabditis elegans

inferredcites →https://doi.org/10.1016/0012-1606(83)90201-4openalex-snapshot

The embryonic cell lineage of the nematode Caenorhabditis elegans

inferredcites →https://doi.org/10.1016/j.ajhg.2017.05.013openalex-snapshot

Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life

inferredcites →https://doi.org/10.1016/j.cell.2012.09.035openalex-snapshot

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

inferredcites →https://doi.org/10.1016/j.cell.2020.05.039openalex-snapshot

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

inferredcites →https://doi.org/10.1016/j.immuni.2016.02.024openalex-snapshot

Tissue-Resident Macrophage Ontogeny and Homeostasis

inferredcites →https://doi.org/10.1016/j.neuron.2014.12.028openalex-snapshot

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

inferredcites →https://doi.org/10.1016/j.stem.2018.01.010openalex-snapshot

CD157 Marks Tissue-Resident Endothelial Stem Cells with Homeostatic and Regenerative Properties

inferredcites →https://doi.org/10.1016/s0140-6736(02)09838-0openalex-snapshot

Genetic heterogeneity of single disseminated tumour cells in minimal residual cancer

inferredcites →https://doi.org/10.1021/acssynbio.6b00309openalex-snapshot

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

inferredcites →https://doi.org/10.1038/nature13448openalex-snapshot

Genome sequencing of normal cells reveals developmental lineages and mutational processes

inferredcites →https://doi.org/10.1038/nature20777openalex-snapshot

Synthetic recording and in situ readout of lineage information in single cells

inferredcites →https://doi.org/10.1038/nbt.2720openalex-snapshot

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

inferredcites →https://doi.org/10.1038/nbt.3637openalex-snapshot

Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq

inferredcites →https://doi.org/10.1038/nbt.4103openalex-snapshot

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

inferredcites →https://doi.org/10.1038/nbt.4124openalex-snapshot

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

inferredcites →https://doi.org/10.1038/ng.3361openalex-snapshot

Exome sequencing identifies recurrent mutations in NF1 and RASopathy genes in sun-exposed melanomas

inferredcites →https://doi.org/10.1038/nmeth.2918openalex-snapshot

Large-scale de novo DNA synthesis: technologies and applications

inferredcites →https://doi.org/10.1038/nmeth.4108openalex-snapshot

Rapidly evolving homing CRISPR barcodes

inferredcites →https://doi.org/10.1038/nmeth.4267openalex-snapshot

Genome-wide profiling of heritable and de novo STR variations

inferredcites →https://doi.org/10.1038/nrg.2016.159openalex-snapshot

Building a lineage from single cells: genetic techniques for cell lineage tracking

inferredcites →https://doi.org/10.1038/nrg3542openalex-snapshot

Single-cell sequencing-based technologies will revolutionize whole-organism science

inferredcites →https://doi.org/10.1038/s41576-020-0223-2openalex-snapshot

Lineage tracing meets single-cell omics: opportunities and challenges

inferredcites →https://doi.org/10.1038/s41586-018-0043-0openalex-snapshot

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

inferredcites →https://doi.org/10.1038/s41592-020-0802-3openalex-snapshot

Integrating lineage tracing and single-cell analysis

inferredcites →https://doi.org/10.1056/nejmoa1408617openalex-snapshot

Age-Related Clonal Hematopoiesis Associated with Adverse Outcomes

inferredcites →https://doi.org/10.1073/pnas.0601265103openalex-snapshot

Phylogenetic fate mapping

inferredcites →https://doi.org/10.1073/pnas.1018981108openalex-snapshot

High-quality DNA sequence capture of 524 disease candidate genes

inferredcites →https://doi.org/10.1073/pnas.96.8.4494openalex-snapshot

Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells

inferredcites →https://doi.org/10.1093/nar/gku1188openalex-snapshot

microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes

inferredcites →https://doi.org/10.1093/nar/gku212openalex-snapshot

Large-scale analysis of tandem repeat variability in the human genome

inferredcites →https://doi.org/10.1093/nar/gky1318openalex-snapshot

Short tandem repeat stutter model inferred from direct measurement ofin vitrostutter noise

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

inferredcites →https://doi.org/10.1101/186940openalex-snapshot

Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing

inferredcites →https://doi.org/10.1101/gr.177774.114openalex-snapshot

The landscape of human STR variation

inferredcites →https://doi.org/10.1101/gr.182212.114openalex-snapshot

MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

inferredcites →https://doi.org/10.1101/gr.202903.115openalex-snapshot

A generic, cost-effective, and scalable cell lineage analysis platform

inferredcites →https://doi.org/10.1126/science.7522346openalex-snapshot

Padlock Probes: Circularizing Oligonucleotides for Localized DNA Detection

inferredcites →https://doi.org/10.1126/science.aab1785openalex-snapshot

Somatic mutation in single human neurons tracks developmental and transcriptional history

inferredcites →https://doi.org/10.1126/science.aaf7907openalex-snapshot

Whole-organism lineage tracing by combinatorial and cumulative genome editing

inferredcites →https://doi.org/10.1126/science.aak9787openalex-snapshot

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

inferredcites →https://doi.org/10.1146/annurev-genom-090413-025352openalex-snapshot

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications

inferredcites →https://doi.org/10.1146/annurev.cb.11.110195.000445openalex-snapshot

Vasculogenesis

inferredcites →https://doi.org/10.1158/0008-5472.can-07-6216openalex-snapshot

Cell Lineage Analysis of a Mouse Tumor

inferredcites →https://doi.org/10.1158/0008-5472.can-15-2998openalex-snapshot

Endothelial Side Population Cells Contribute to Tumor Angiogenesis and Antiangiogenic Drug Resistance

inferredcites →https://doi.org/10.1158/1078-0432.ccr-04-1995openalex-snapshot

Detection of Melanoma Cells Displaying Multiple Genomic Changes in Histopathologically Negative Sentinel Lymph Nodes

inferredcites →https://doi.org/10.1182/blood-2011-10-388629openalex-snapshot

Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and microsatellite instability

inferredcites →https://doi.org/10.1182/blood-2017-02-769869openalex-snapshot

Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly

inferredcites →https://doi.org/10.1186/gm454openalex-snapshot

Multiplex target capture with double-stranded DNA probes

inferredcites →https://doi.org/10.1371/journal.pcbi.0010050openalex-snapshot

Genomic Variability within an Organism Exposes Its Cell Lineage Tree

inferredcites →https://doi.org/10.1371/journal.pgen.1007108openalex-snapshot

Aging and the rise of somatic cancer-associated mutations in normal tissues

inferredcites →https://doi.org/10.1371/journal.pmed.1001604openalex-snapshot

Quantitative Measurement of Melanoma Spread in Sentinel Lymph Nodes and Survival

inferredcites →https://doi.org/10.1371/journal.pone.0001939openalex-snapshot

Reconstruction of Cell Lineage Trees in Mice

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0085907openalex-snapshot

Reliable Single Cell Array CGH for Clinical Samples

inferredcites →https://doi.org/10.15252/emmm.201404033openalex-snapshot

Molecular profiling of single circulating tumor cells with diagnostic intention

inferredcites →https://doi.org/10.4137/ebo.s9657openalex-snapshot

TreeCmp: Comparison of Trees in Polynomial Time

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-1-0716-4310-5_2openalex-snapshot

Tracking Somatic Mutations for Lineage Reconstruction

inferred← citeshttps://doi.org/10.1007/s11427-024-2751-6openalex-snapshot

The landscape of cell lineage tracing

inferred← citeshttps://doi.org/10.1146/annurev-genom-111320-090436openalex-snapshot

Applications of Single-Cell DNA Sequencing

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3083262/v1openalex-snapshot

Mitochondrial mutation, drift and selection during human development and ageing

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