Separation Of cfDNA With The Agilent HS NGS Kit On The Agilent Fragment Analyzer Systems

By Chava Pocernich, Whitney Pike, and Kit-Sum Wong, Agilent Technologies, Inc.

Circulating cell-free DNA (cfDNA) has become an essential analyte for applications such as liquid biopsy, fetal screening, and next‑generation sequencing (NGS) library preparation. Understanding its size distribution—and distinguishing it from contaminants like genomic DNA or carrier RNA—is critical for confident downstream analysis. This application note explores how high‑sensitivity capillary electrophoresis enables clear visualization of key cfDNA features, including mono‑, di‑, and trinucleosome peaks, while also identifying common interferences. It highlights how different extraction methods influence sample purity and demonstrates how run conditions and array formats affect separation quality and speed. Gain practical insight into optimizing cfDNA QC, selecting workflows that minimize artifacts, and ensuring cleaner data for sensitive genomics applications.

Examine detailed separation profiles, method comparisons, and practical considerations for improving cfDNA analysis.