Table 2.

Comparison of different biomarker types, along with the information they contain, the most widely used detection method and their advantages and disadvantages. Abbreviations: ccfDNA (circulating cell-free DNA); CTC (circulating tumor cells); ELISA (enzyme-linked immunosorbent assay); EV (extracellular vesicle); FISH (fluorescence in-situ hybridization); IHC (immunohistochemistry); NGS (next-generation sequencing); qPCR (quantitative polymerase chain reaction); RNA-Seq (RNA sequencing); RT-qPCR (reverse transcription quantitative real-time polymerase chain reaction).

Type of Biomarker	Sample Type	Information	Detection Methods (i.a.)	Advantages	Disadvantages
Proteins [16]	Tissue biopsies	Expression pattern in tissue of interest	ELISA IHC Immunoblotting Flow Cytometry	Direct mediators of cellular changes Well-established biomarkers and assays available	Expensive antibody-based detection In most cases invasive sampling necessary
	Liquid biopsies (body fluids): blood, urine, saliva, i.a.	Systemic expression information	ELISA IHC Immunoblotting Flow Cytometry	Direct mediators of cellular changes High-throughput methods available Minimal invasive sampling	Expensive antibody-based detection Tissue of origin not determined
Intracellular RNA [15,66]	Tissue biopsies	Expression pattern in tissue of interest	RT-qPCR RNA-Seq Microarrays FISH	Expression-level analysis Detection of ncRNA	In most cases invasive sampling necessary
	Liquid biopsies: blood	Systemic expression information	RT-qPCR RNA-Seq Microarrays	Expression-level analysis Immunophenotyping Analysis of ncRNA Minimal invasive sampling	Tissue of origin not determined Almost exclusively information about immune response
Extracellular RNA, e.g., EV-associated [15,67,68]	Liquid biopsies (body fluids): blood, urine, saliva, i.a.	Systemic expression information	RT-qPCR RNA-Seq Microarrays	Semi-direct information Analysis of ncRNA Minimal invasive sampling	Fragmented Relatively new (few biomarkers and assays established) Only partial transcriptome Tissue of origin not determined
Genomic DNA [8,69]	Tissue biopsies	Mutations in the tissue of interest Epigenetic status in tissue of interest	qPCR NGS	Complete genome of the tissue of interest	Only indirect expression information available In most cases invasive sampling necessary
	Liquid biopsies (body fluids): blood, urine, saliva, i.a.	Mutations in the tissue of interest Epigenetic status in tissue of interest	qPCR NGS	Not limited to a certain tissue Minimal invasive sampling	Only limited gene expression information No information about tissue of origin
ccfDNA [6,18,67,70]	Liquid biopsies (body fluids): blood, urine, saliva, i.a.	Mutations throughout the whole body	qPCR NGS	Minimal invasive sampling	No expression information available Fragmented
CTCs [6,7,18]	Liquid biopsies: blood, urine	Metastatic tumor cells	Flow Cytometry (RT-)qPCR NGS	Minimal invasive sampling Tumor DNA, RNA and proteins combined	Less useful in later tumor stages Limited to tumor diagnosis