ArticlePloS one2016
A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 50 citations in OpenAlex.
- Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA.Genome medicine · 2019Trial
- New Candidate Reference Measurement Procedures for MET CNV Detection and Quantification Using Digital PCR.Biological procedures online · 2026Article
- Comparative Analysis of Concentration and Quantification Methods for Antibiotic Resistance Genes and Their Phage-Mediated Dissemination in Treated Wastewater and Biosolids.Pathogens (Basel, Switzerland) · 2025Article
- Droplet digital PCR assay for precise determination of FRS2 gene copy number in bladder cancer.BMC cancer · 2025Article
- High-dimensional droplet digital PCR of multiple hepatitis B splice variants in serum, liver, and tissue culture.Journal of virological methods · 2025Article
- Optimizing C-Type Natriuretic Peptide and Receptor Expression Analysis with Droplet Digital™ PCR: Advancing Biomarker Discovery for Brugada Syndrome?Biomolecules · 2025Article
- Advancing artemisinin resistance monitoring using a high sensitivity ddPCR assay for Pfkelch13 mutation detection in Asia.Scientific reports · 2025Article
- The known structural variations in hearing loss and their diagnostic approaches: a comprehensive review.Molecular biology reports · 2025Review
- Benchmarking digital PCR partition classification methods with empirical and simulated duplex data.Briefings in bioinformatics · 2024Article
- Detection ofBiomedicines · 2024Article
- Clinically accessible amplitude-based multiplex ddPCR assay for tryptase genotyping.Scientific reports · 2024Article
- Inoculum dose-disease response relationships for the pea root rot pathogen,Frontiers in plant science · 2023Article
- Digital PCR-Based Method for Detecting CDKN2A Loss in Brain Tumours.Molecular diagnosis & therapy · 2022Article
- An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens.Frontiers in microbiology · 2022Article
- Development and Evaluation of a Droplet Digital PCR Assay for 8p23 β-Defensin Cluster Copy Number Determination.Molecular diagnosis & therapy · 2021Article
- Measurement of gene amplifications related to drug resistance in Plasmodium falciparum using droplet digital PCR.Malaria journal · 2021Article
- Identification of a Clinical Cutoff Value for Multiplex KRASJournal of clinical medicine · 2020Article
- Digital polymerase chain reaction for detecting c-MYC copy number gain in tissue and cell-free plasma samples of colorectal cancer patients.Scientific reports · 2019Article
- Using ddPCR to assess the DNA yield of FFPE samples.Biomolecular detection and quantification · 2018Article
- ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ability of droplet digital PCR (ddPCR) to accurately determine the concentrations of amplifiable targets makes it a promising platform for measuring copy number alterations (CNAs) in genomic biomarkers. However, its application to clinical samples, particularly formalin-fixed paraffin-embedded specimens, will require strategies to reliably determine CNAs in DNA of limited quantity and quality. When applied to cancerous tissue, those methods must also account for global genetic instability and the associated probability that the abundance(s) of one or more chosen reference loci do not represent the average ploidy of cells comprising the specimen. Here we present an experimental design strategy and associated data analysis tool that enables accurate determination of CNAs in a panel of biomarkers using multiplexed ddPCR. The method includes strategies to optimize primer and probes design to cleanly segregate droplets in the data output from reaction wells amplifying multiple independent templates, and to correct for bias from artifacts such as DNA fragmentation. We demonstrate how a panel of reference loci can be used to determine a stable CNA-neutral benchmark. These innovations, when taken together, provide a comprehensive strategy that can be used to reliably detect biomarker CNAs in DNA extracted from either frozen or FFPE tissue biopsies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.