High-resolution insertion-site analysis by linear amplification-mediated PCR (LAM-PCR)
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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- 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
- Licence
- www.springer.com/tdm (tdm)
- 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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