ArticleBMC biology2020
CloneSifter: enrichment of rare clones from heterogeneous cell populations.
Article in BMC biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 26 citations in OpenAlex.
- A multi-kingdom genetic barcoding system for precise clone isolation.Nature biotechnology · 2026Article
- Strength through diversity: how cancers thrive when clones cooperate.Molecular oncology · 2026Review
- Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.Nature communications · 2025Article
- Single-Cell Lineage Tracing and Clonal State-Fate Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Advancements in prospective single-cell lineage barcoding and their applications in research.Genome research · 2024Review
- High-throughput retrieval of target sequences from complex clone libraries using CRISPRi.Nature biotechnology · 2023Article
- Integration of quantitative methods and mathematical approaches for the modeling of cancer cell proliferation dynamics.American journal of physiology. Cell physiology · 2023Review
- Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAFCell discovery · 2022Article
- Clonal barcoding with qPCR detection enables live cell functional analyses for cancer research.Nature communications · 2022Article
- Article
- Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer.Frontiers in immunology · 2022Article
- Applications of high-resolution clone tracking technologies in cancer.Current opinion in biomedical engineering · 2021Article
- Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment.Nature cancer · 2021Article
- Article
- Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway.Cancer cell · 2020Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundMany biological processes, such as cancer metastasis, organismal development, and acquisition of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. While large-scale barcoding with NGS readout has facilitated cellular fitness assessment at the population level, this approach does not support characterization of clones prior to selection. Single-cell genomics methods provide high biological resolution, but are challenging to scale across large populations to probe rare clones and are destructive, limiting further functional analysis of important clones.
resultsHere, we develop CloneSifter, a methodology for tracking and enriching rare clones throughout their response to selection. CloneSifter utilizes a CRISPR sgRNA-barcode library that facilitates the isolation of viable cells from specific clones within the barcoded population using a sequence-specific retrieval reporter. We demonstrate that CloneSifter can measure clonal fitness of cancer cell models in vitro and retrieve targeted clones at abundance as low as 1 in 1883 in a heterogeneous cell population.
conclusionsCloneSifter provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.