Ultra-sensitive Cancer Liquid Biopsy NGS Analysis with the Agilent SureSelectXT HS Target Enrichment Workflow

Low input cfDNA sequencing and molecular barcode error correction with
Agilent SureSelectXT HS technology unlocks mutation and DNA copy number
profiles of liquid biopsies.
Introduction
Circulating free DNA (cfDNA) sequencing allows minimally invasive genetic
profiling of cancers and the detection of subclonal genetic variants which
are frequently missed by single biopsies in heterogeneous cancers. Tumour
derived DNA content within the cfDNA is low in many cancer types (<5%), with subclonal variants reaching even lower variant frequencies (often <1%). Mutation discovery in cfDNA hence requires highly sensitive and specific techniques to identify rare variants with confidence. Solution-phase hybridization capture sequencing allows simultaneous investigation of nucleotide level variation, copy number aberrations and translocations across target gene panels, but detection of rare variants has previously been limited by PCR and sequencing error rates. Application of Agilent SureSelectXT HS technology, which integrates molecular barcodes (MBC) for sequencing error correction, achieved highly sensitive (detection limit ~ 0.1%) and easily customizable cfDNA sequencing. The analysis of off-target sequencing reads enabled reconstruction of genome-wide copy number profiles in addition to mutation and copy number changes of target genes.

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