The 1st ctDNA seminar will be about digital PCR data handling
The ctDNA seminars will be held approximately every second month.
The seminars are open for everyone in the ctDNA Center to participate in - so feel free to share it with others who are working with or interested in ctDNA in Denmark.
Everyone in the center can contribute with a workshop in their field of expertise or suggest wishes for a theme for a seminar - contact Anne Lærke Lorentzen,
The seminar series is an element of the ctDNA Research Center’s aim to facilitate national collaboration regarding research on ctDNA guided cancer treatment.
Seminar: Digital PCR data handling
Date: 25 January 2023
Time: 3:00 pm - 5:30 pm (Kl. 15:00-17:30)
Place: Online at Zoom (link will follow in an e-mail after registration deadline)
Seminar leader: Tenna Henriksen, Postdoc at Department of Molecular Medicine (MOMA) Aarhus University and Aarhus University Hospital
Target population: Everybody who uses ddPCR for ctDNA detection
Registration: Please register here (Registration deadline is the 20th of January 2023)
Purpose:
Many studies involving circulating tumor DNA (ctDNA) detection are using digital PCR (dPCR) to quantify ctDNA. One of the attractive qualities of dPCR is the relatively simple data output format, enabling easy data processing. Yet, dPCR is – like all molecular tools – susceptible to noise, which can complicate quantification of low ctDNA levels. This online workshop will introduce basic data handling of dPCR data and via practical exercises guide participants through the steps of correcting for noise in dPCR data. Finally, the workshop will showcase examples of how substandard data handling can lead to problematic study results.
Learning outcomes:
- Defining positive and negative droplets
- Applying different methods to differentiate between noise and signal
- Understanding factors impacting the noise level in cfDNA analysis
- Understanding the requirements for various noise-correction methods
- Discern which noise-correction method is suitable for different studies
- Appreciate the implications of false-positives and false-negatives on a real-life study
Requirements:
- Basic understanding of digital PCR and what the data represents
- R-studio and R installed on the computer prior to the workshop
- Following packages installed in R: “dplyr” and “ggplot2”
- If possible, access to a computer running the QuantaSoft Software from BioRad. If this is not possible accommodations will be made on the day.
Preparation:
- Install R and R-studio on your computer
- Read paper: “Error Characterization and Statistical Modeling Improves Circulating Tumor DNA Detection by Droplet Digital PCR” by Henriksen et al. (https://doi.org/10.1093/clinchem/hvab274).