Table 1.

Comparison of different analytical approaches for study of cfDNA

	Coverage	Output	Turnaround time from taking sample	Suggested minimum cfNA input	Relative complexity of analysis and clinical interpretation	Relative cost £-££££	Fragment information preserved?
Genomic analyses
ddPCR	1 mutation hotspot/assay	VAF (quantitative)	2–5 days	0.1 ng/well	Low	£	No
Targeted NGS	Up to 1000 genes	Base pair sequence	1–2 weeks	10 ng	Medium	££	At selected regions only for hybrid capture-based methods
WES	All protein coding regions (∼1.5% genome)	Base pair sequence, copy-number changes	2 weeks	10 ng	Medium-High	£££	At exome only
WGS	Whole genome	Base pair sequence, copy-number changes	2–3 weeks	10 ng	High	££££	Yes
Methylation analyses
Bisulfite conversion based sequencing	Up to whole methylome but loss of 84–96% DNA	Methylation status at base pair level.	2 weeks	10 ng, ideally more for WGBS	High	££-£££a	At regions covered
Methylation capture-based enrichment	Genome-wide methylation	Methylation status at fragment level (5-mC only)	2–3 weeks	1 ng	High	£££	Only for enriched methylated regions
Enzyme-based methylation (e.g., EM-seq, TAPs)	Up to whole methylome	Methylation status at base pair level.	2–3 weeks	10 ng	High	£££-££££a	Yes
Combined genomic and methylation analyses
5/6 letter sequencing (Duet)	Up to whole methylome/whole genome	5-mC/5-hMC status at base pair level. Preserves base pair sequence.	2–3 weeks	5 ng	High	£££- ££££a	Partially, dependent on read length
Native DNA sequencing e.g., nanopore	Up to whole methylome/whole genome	5-mC/5-hMC status at base pair level. Preserves base pair sequence. Sequences longer fragments	24–48 h	5 ng	High	£££-££££a	Yes
Transcriptomic analyses
ddPCR	1 gene/assay	VAF (quantitative)	2–5 days	0.1 ng/well	Low	£	No
Targeted panel	Up to 1000 genes	Base pair sequence, fusions	1–2 weeks	10 ng	Medium	££	n/a
RNA-seq (whole exome/whole transcriptome)	All protein coding (exome)/transcribed regions	Base pair sequence, copy-number changes	2 weeks	10 ng	Medium-High	£££	n/a

VAF, variant allele frequency; ddPCR, digital droplet polymerase chain reaction; NGS, next-generation sequencing; WGS, whole-genome sequencing; WES, whole-exome sequencing.

^aCost varies dependent on sequencing coverage and depth.