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Minimally invasive liquid biopsies have recently emerged as novel diagnostic methods which hold the promise to monitor disease progression, detect minimal residual disease, therapy resistance and potentially even early cancer detection. Participants will gain hands-on experience in the detection of cell free tumor DNA (cfDNA) using a next generation sequencing (NGS) approach that covers all four mutation classes in a single assay. Critical aspects on recent developments to increase analytical sensitivity and mitigate sequencing errors (computational error correction) will be discussed as well as annotation, interpretation, and clinical reporting of liquid biopsy tests. Lectures will cover the evaluation of ctDNA as biomarkers, clinical applications, emerging analytes for liquid biopsy and important challenges.
The course is aimed at scientists, clinical scientists, molecular pathologists and industry researchers who would like to learn about possible applications and want to gain hands-on experience in the field of liquid biopsy from sample acquisition, target enrichment, analysis and interpretation.
- Possible use cases of nucleic acids in blood and plasma in clinical settings
- Strategies for the construction of high quality NGS libraries from challenging cfDNA samples (sample and molecular barcoding, low input amounts, quality controls)
- In-solution hybridization based target enrichment of clinically relevant targets, covering all four mutation classes in a single assay (SNVs, fusions, indels, CNVs)
- Bioinformatics analysis including integrated digital error suppression (iDES), variant calling and reporting
- Annotation, interpretation of mutations and clinical reporting (therapy matching and optional clinical decision support)
- Understanding of potential applications for liquid biopsy in clinical care
- Challenges that must be overcome before liquid biopsies can be applied in precision medicine
- Overview of emerging liquid biopsy methods and markers
- Ability to handle cfDNA, generate NGS libraries, enrich targets of interest, annotate and interprate of variants and their frequences