DLMDA pre-amplification preserves genome-wide copy-number profiles in FFPE samples despite reduced detection sensitivity

Whole-genome sequencing (WGS) enables comprehensive analysis of tumour genomes, but its use in formalin-fixed paraffin-embedded (FFPE) samples is limited by DNA fragmentation and low yields. Whole-genome amplification (WGA) methods such as multiple displacement amplification (MDA) can boost DNA availability but distort copy-number alteration (CNA) profiles. DNA ligation-mediated MDA (DLMDA) mitigates this bias by reconstituting fragmented templates, yet its performance in FFPE-derived DNA remains uncertain. We compared paired DLMDA pre-amplified (2h, 8h) and non-pre-amplified FFPE prostate tumour samples from 15 archival blocks (5, 15 and 20years old). DLMDA increased DNA yield by 7.3–15.4-fold, with global CNA patterns largely preserved. However, DLMDA significantly reduced the detected total CNA burden from 10.4% (baseline) to 4.6% after 2h and 7.6% after 8h pre-amplification, independently of FFPE sample age. CNA dropouts were randomly distributed across the genome, indicating that DLMDA does not introduce regional bias. Our results show that DLMDA enables robust DNA yield recovery and avoids false-positive CNA artefacts, suggesting DLMDA can be used as rescue strategy for poor quality, low yield, FFPE-derived DNA, but at the cost of reduced CNA sensitivity. While suitable for CNA screening pipelines through WGS, further improvements are required to minimise the false-negative risk and improve the technique’s sensitivity for FFPE-based genomics.