ArticleJournal of virology2010
High-throughput, sensitive quantification of repopulating hematopoietic stem cell clones.
Article in Journal of virology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- Mapping Hematopoietic Fate after Transplantation.Stem cell reviews and reports · 2025Review
- Clonal abundance patterns in hematopoiesis: Mathematical modeling and parameter estimation.Frontiers in systems biology · 2023Article
- Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias.Stem cell research & therapy · 2021Article
- Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque.PLoS computational biology · 2018Article
- Purging Exhausted Virus-Specific CD8 T Cell Phenotypes by Somatic Cell Reprogramming.AIDS research and human retroviruses · 2017Article
- Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow.Journal of visualized experiments : JoVE · 2017Article
- Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques.BMC biology · 2015Article
- Quantitative shearing linear amplification polymerase chain reaction: an improved method for quantifying lentiviral vector insertion sites in transplanted hematopoietic cell systems.Human gene therapy methods · 2015Article
- Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo.Genome biology · 2014Article
- Dynamics of HSPC repopulation in nonhuman primates revealed by a decade-long clonal-tracking study.Cell stem cell · 2014Article
- No impact of lentiviral transduction on hematopoietic stem/progenitor cell telomere length or gene expression in the rhesus macaque model.Molecular therapy : the journal of the American Society of Gene Therapy · 2014Article
- Evaluating a ligation-mediated PCR and pyrosequencing method for the detection of clonal contribution in polyclonal retrovirally transduced samples.Human gene therapy methods · 2013Article
- Counting stem cells: methodological constraints.Nature methods · 2012Article
- Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding.Nature biotechnology · 2011Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Retroviral vector-mediated gene therapy has been successfully used to correct genetic diseases. However, a number of studies have shown a subsequent risk of cancer development or aberrant clonal growths due to vector insertion near or within proto-oncogenes. Recent advances in the sequencing technology enable high-throughput clonality analysis via vector integration site (VIS) sequencing, which is particularly useful for studying complex polyclonal hematopoietic progenitor/stem cell (HPSC) repopulation. However, clonal repopulation analysis using the current methods is typically semiquantitative. Here, we present a novel system and standards for accurate clonality analysis using 454 pyrosequencing. We developed a bidirectional VIS PCR method to improve VIS detection by concurrently analyzing both the 5' and the 3' vector-host junctions and optimized the conditions for the quantitative VIS sequencing. The assay was validated by quantifying the relative frequencies of hundreds of repopulating HPSC clones in a nonhuman primate. The reliability and sensitivity of the assay were assessed using clone-specific real-time PCR. The majority of tested clones showed a strong correlation between the two methods. This assay permits high-throughput and sensitive assessment of clonal populations and hence will be useful for a broad range of gene therapy, stem cell, and cancer research applications.
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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.