ArticleNucleic acids research2015
Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ.
Article in Nucleic acids research, 2015. 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, 33 citations in OpenAlex.
- Spatial profiling of gene editing by in situ sequencing in mice and macaques.Nature biomedical engineering · 2026Article
- A Simple and Fast Optical Clearing Method for Whole-Mount Fluorescence In Situ Hybridization (FISH) Imaging.Journal of biophotonics · 2025Article
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- Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes.Nature biomedical engineering · 2023Article
- Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.Genome biology · 2023Article
- Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects.Frontiers in molecular biosciences · 2023Review
- The emerging landscape of spatial profiling technologies.Nature reviews. Genetics · 2022Review
- Review
- Isothermal amplification-assisted diagnostics for COVID-19.Biosensors & bioelectronics · 2022Review
- Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping.Accounts of chemical research · 2021Review
- Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations.RSC advances · 2018Article
- Article
- Interlinked DNA nano-circles for measuring topoisomerase II activity at the level of single decatenation events.Nucleic acids research · 2017Article
- HistoMosaic Detecting KRAS G12V Mutation Across Colorectal Cancer Tissue Slices through in Situ PCR.Analytical chemistry · 2016Article
- The niche in single-cell technologies.Immunology and cell biology · 2016Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In clinical diagnostics a great need exists for targeted in situ multiplex nucleic acid analysis as the mutational status can offer guidance for effective treatment. One well-established method uses padlock probes for mutation detection and multiplex expression analysis directly in cells and tissues. Here, we use oligonucleotide gap-fill ligation to further increase specificity and to capture molecular substrates for in situ sequencing. Short oligonucleotides are joined at both ends of a padlock gap probe by two ligation events and are then locally amplified by target-primed rolling circle amplification (RCA) preserving spatial information. We demonstrate the specific detection of the A3243G mutation of mitochondrial DNA and we successfully characterize a single nucleotide variant in the ACTB mRNA in cells by in situ sequencing of RCA products generated by padlock gap-fill ligation. To demonstrate the clinical applicability of our assay, we show specific detection of a point mutation in the EGFR gene in fresh frozen and formalin-fixed, paraffin-embedded (FFPE) lung cancer samples and confirm the detected mutation by in situ sequencing. This approach presents several advantages over conventional padlock probes allowing simpler assay design for multiplexed mutation detection to screen for the presence of mutations in clinically relevant mutational hotspots directly in situ.
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