Get More From Less: AMP Chemistry Outperforms Hybrid Capture For Degraded, Low Input FFPE Tumor DNA

This content is brought to you by Integrated DNA Technologies, a Danaher Operating Company.

Reliable sequencing from FFPE tumor samples often hinges on how well workflows handle degraded, low-input DNA. A head-to-head comparison of enrichment approaches reveals meaningful differences when sample quality and quantity become limiting. Anchored Multiplex PCR (AMP) maintains strong quality control performance and more consistent variant recovery where hybrid capture begins to struggle, particularly below 10 ng input. The data shows fewer QC failures, higher recovery of expected SNV/indel variants, and closer alignment with orthogonal allele frequency benchmarks under challenging conditions. At higher inputs, both methods perform comparably, but AMP extends usability deeper into low-input scenarios, supporting a more unified workflow without sacrificing accuracy.

Access the full white paper to see how chemistry choice impacts real-world sequencing outcomes.