Table 1.

Common pre-analytical and sample preparation issues related to different sample types

Sample type	Common issues	Impact	Contingencies/solutions
Formalin-fixed, paraffin-embedded (FFPE)	• Low yield of DNA • DNA degradation • DNA base modification • RNA degradation	• Reduced complexity libraries; library failure; decreased sensitivity • Reduced complexity; library failure; decreased sensitivity • Increased false positive rate • Library failure; high duplication	• DNA repair; pooling of indexed libraries prior to capture (exomes or panels); specialized low input library methods • DNA repair; short amplicon amplification; specialized library methods • FFPE-aware filtering of variants; DNA repair • Selection-based or targeted preparation instead of polyA-based preparation
Fresh frozen tissue of bulk cells	• Buffer or process-induced modification of DNA bases	• Increased false positive rate	• Chelation of oxidative species; oxidation aware filtering
Single cells	• Low DNA yield • Whole genome amplification (WGA) bias • Low RNA yield	• Library failure • Increased false positives and false negatives • Library failure	• WGA • Optimized WGA • Whole transcriptome amplification (WTA)
Liquid biopsy	• Low DNA yield of cfDNA • Low purity of ctDNA in cfDNA • Low DNA yield from CTCs • Low RNA yield and quality from CTCs • Low RNA yield from EVs	• Library failure; reduced sensitivity • Reduced sensitivity • Library failure; reduced sensitivity; reduced specificity • Library failure • Library failure	• Optimized library preparation; specialized library preparation • High sequencing depth; molecular barcoding (UMIs) • WGA • WTA; specialized library preparation. • WTA; specialized library preparation.