Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ

Journal article

Marco Mignardi, A. Mezger, Xiaoyan Qian, L. La Fleur, J. Botling, Chatarina Larsson, M. Nilsson
Nucleic Acids Research, 2015

Semantic Scholar DOI PubMedCentral PubMed

Cite

APA Click to copy
Mignardi, M., Mezger, A., Qian, X., Fleur, L. L., Botling, J., Larsson, C., & Nilsson, M. (2015). Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ. Nucleic Acids Research.

Chicago/Turabian Click to copy
Mignardi, Marco, A. Mezger, Xiaoyan Qian, L. La Fleur, J. Botling, Chatarina Larsson, and M. Nilsson. “Oligonucleotide Gap-Fill Ligation for Mutation Detection and Sequencing in Situ.” Nucleic Acids Research (2015).

MLA Click to copy
Mignardi, Marco, et al. “Oligonucleotide Gap-Fill Ligation for Mutation Detection and Sequencing in Situ.” Nucleic Acids Research, 2015.

BibTeX Click to copy

@article{marco2015a,
  title = {Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ},
  year = {2015},
  journal = {Nucleic Acids Research},
  author = {Mignardi, Marco and Mezger, A. and Qian, Xiaoyan and Fleur, L. La and Botling, J. and Larsson, Chatarina and Nilsson, M.}
}

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.