Sequencing of cfDNA from plasma sample using hybrid capture duplex sequencing
cfDNA libraries were prepared using the MSK-ACCESS cfDNA protocol. In brief, cfDNA were extracted from plasma (MagMAX cfDNA isolation kit). UMIs and xGen Duplex Seq Adapters with dual index barcodes from IDT (Integrated DNA Technologies) were introduced during library construction. Libraries were pooled in equimolar concentrations and captured using patient specific probe sets from IDT (xGEN MRD). Captured DNA fragments were then sequenced on an Illumina sequencer (HiSeq 2500 or NovaSeq 6000) as paired-end reads.