ArticleNucleic acids research2018
Enhanced detection of microsatellite instability using pre-PCR elimination of wild-type DNA homo-polymers in tissue and liquid biopsies.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 39 citations in OpenAlex.
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- Enzymatic Methods for Mutation Detection in Cancer Samples and Liquid Biopsies.International journal of molecular sciences · 2023Review
- Liquid biopsy approaches to capture tumor evolution and clinical outcomes during cancer immunotherapy.Journal for immunotherapy of cancer · 2023Review
- Microsatellite Instability: From the Implementation of the Detection to a Prognostic and Predictive Role in Cancers.International journal of molecular sciences · 2022Review
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- Current and Future Clinical Applications of ctDNA in Immuno-Oncology.Cancer research · 2022Review
- Clinical Validity of Plasma-Based Genotyping for Microsatellite Instability Assessment in Advanced GI Cancers: SCRUM-Japan GOZILA Substudy.JCO precision oncology · 2022Article
- Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Detection of Microsatellite Instability by High-Resolution Melting Analysis in Colorectal CancerIranian biomedical journal · 2022Article
- Review
- Detection of Microsatellite Instability: State of the Art and Future Applications in Circulating Tumour DNA (ctDNA).Cancers · 2021Review
- Microsatellite Instability in Colorectal Cancer Liquid Biopsy-Current Updates on Its Potential in Non-Invasive Detection, Prognosis and as a Predictive Marker.Diagnostics (Basel, Switzerland) · 2021Review
- NGS-based identification and tracing of microsatellite instability from minute amounts DNA using inter-Alu-PCR.Nucleic acids research · 2021Article
- Sensitive detection of microsatellite instability in tissues and liquid biopsies: Recent developments and updates.Computational and structural biotechnology journal · 2021Review
- PCR past, present and future.BioTechniques · 2020Review
- SLAM-MS: Mutation scanning of stem-loop amplicons with TaqMan probes by quantitative DNA melting analysis.Scientific reports · 2020Article
- A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment.Nucleic acids research · 2019Article
- Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer.Nucleic acids research · 2019Article
- Noninvasive Detection of Microsatellite Instability and High Tumor Mutation Burden in Cancer Patients Treated with PD-1 Blockade.Clinical cancer research : an official journal of the American Association for Cancer Research · 2019Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Detection of microsatellite-instability in colonoscopy-obtained polyps, as well as in plasma-circulating DNA, is frequently confounded by sensitivity issues due to co-existing excessive amounts of wild-type DNA. While also an issue for point mutations, this is particularly problematic for microsatellite changes, due to the high false-positive artifacts generated by polymerase slippage (stutter-bands). Here, we describe a nuclease-based approach, NaME-PrO, that uses overlapping oligonucleotides to eliminate unaltered micro-satellites at the genomic DNA level, prior to PCR. By appropriate design of the overlapping oligonucleotides, NaME-PrO eliminates WT alleles in long single-base homopolymers ranging from 10 to 27 nucleotides in length, while sparing targets containing variable-length indels at any position within the homopolymer. We evaluated 5 MSI targets individually or simultaneously, NR27, NR21, NR24, BAT25 and BAT26 using DNA from cell-lines, biopsies and circulating-DNA from colorectal cancer patients. NaME-PrO enriched altered microsatellites and detected alterations down to 0.01% allelic-frequency using high-resolution-melting, improving detection sensitivity by 500-1000-fold relative to current HRM approaches. Capillary-electrophoresis also demonstrated enhanced sensitivity and enrichment of indels 1-16 bases long. We anticipate application of this highly-multiplex-able method either with standard 5-plex reactions in conjunction with HRM/capillary electrophoresis or massively-parallel-sequencing-based detection of MSI on numerous targets for sensitive MSI-detection.
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Registered trials
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