Cited by 328Virus-based gene therapy researchCRISPR and Genetic EngineeringAnimal Genetics and Reproduction

High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR)

Schmidt, Manfred, Schwarzwaelder, Kerstin, Bartholomae, Cynthia, Zaoui, Karim, Ball, Claudia, Pilz, Ingo, Braun, Sandra, Glimm, Hanno +1 more·2007·Nature Methods

Abstract

Integrating vector systems used in clinical gene therapy have proven their therapeutic potential in the long-term correction of immunodeficiencies. The integration loci of such vectors in the cellular genome represent a molecular marker unique for each transduced cell and its clonal progeny. To gain insight into the physiology of gene-modified hematopoietic repopulation and vector-related influences on clonal contributions, we have previously introduced a technology--linear amplification-mediated (LAM) PCR--for detecting and sequencing unknown DNA flanking sequences down to the single cell level (Supplementary Note online). LAM-PCR analyses have enabled qualitative and quantitative measurements of the clonal kinetics of hematopoietic regeneration in gene transfer studies, and uncovered the clonal derivation of non-leukemogenic and leukemogenic insertional side effects in preclinical and clinical gene therapy studies. The reliability and robustness of this method results from the initial preamplification of the vector-genome junctions preceding nontarget DNA removal via magnetic selection. Subsequent steps are carried out on a semisolid streptavidin phase, including synthesis of double complementary strands, restriction digest, ligation of a linker cassette onto the genomic end of the fragment and exponential PCR(s) with vector- and linker cassette-specific primers. LAM-PCR can be adjusted to all unknown DNA sequences adjacent to a known DNA sequence. Here we describe the use of LAM-PCR analyses to identify 5' long terminal repeat (LTR) retroviral vector adjacent genomic sequences.

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Crossref · 10.1038/nmeth1103

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  • Extended gRNA GGX20 decreases off-target effects.

    “Extended gRNA: GGX20 | Decreased off-target effects”

    From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [74]

  • Truncated gRNA truncated by 2-3 bp at the 5' end decreases off-target effects.

    “Truncated gRNA: truncated by 2-3bp at 5’ end | Decreased off-target effects”

    From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [74]

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Authors
Schmidt, M., Schwarzwaelder, K., Bartholomae, C., Zaoui, K., Ball, C., Pilz, I., Braun, S., Glimm, H., & von Kalle, C.
Affiliations
  • German Cancer Research Center (DE)
  • National Center for Tumor Diseases (DE)
  • University Medical Center Freiburg (DE)
  • University of Freiburg (DE)
Corresponding author
Schmidt, Manfred
Venue
Nature Methods
Published
2007-12
Volume
4
Issue
12
Pages
1051-1057
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W2136139751
Cited by
328
References
10
Citations by year
2026: 5 · 2025: 9 · 2024: 16 · 2023: 12 · 2022: 13 · 2021: 12 · 2020: 19 · 2019: 10 · 2018: 10 · 2017: 24 · 2016: 24 · 2015: 22 · 2014: 31 · 2013: 17 · 2012: 34
FWCI
7.47
Type
journal article
Language
en
Open access
closed
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
Funders
Deutsche Forschungsgemeinschaft
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Animal Genetics and Reproduction
Keywords
retroviral vectors, long terminal repeat, gene therapy vectors, hematopoietic repopulation, leukemogenesis, single-cell sequencing
MeSH terms
Base Sequence, Chromosome Mapping, DNA Transposable Elements, Genetic Markers, Molecular Sequence Data, Polymerase Chain Reaction, Sequence Alignment, Sequence Analysis, DNA

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