Cell free DNA from plasma at baseline or progression timepoints from participants with mCRPC enrolled in Alliance A031201 trial, sample OM108867_P from subject SUBJ384 and sequencing library 102.
Cell-free DNA (cfDNA) was isolated from 1-3 mL of input plasma using a Circulating Nucleic Acid kit (Qiagen catalog 55114) and library was created with the ThruPLEX Plasma-Seq kit (Takara, Catalog R400681). Targeted DNA-seq was performed using SureSelect (Agilent Technologies) capture protocol (Version B.3 June 2015). Libraries were hybridized overnight (between 16 - 24 hours) using a SureSelect XT Reagent Kit (Agilent, Catalog 930672) and SureSelect XT Custom Baits (Agilent, Catalog 5191-6908). Libraries were pooled in equimolar amounts for sequencing using an Illumina NovaSeq 6000 SP flow cell with 2x150 bp settings.