Whole Genome Sequencing of Pancreatic CTCs and Cell Lines

The goal of the study was to design an integrated workflow for the antigen agnostic isolation of pancreatic circulating tumor cells (CTCs) from blood with subsequent whole genome sequencing and CNV analysis. Pancreatic cancer cells from established cell lines (Panc1, BxPC3, and Capan2), as well as two expanded CTC-derived cell lines were processed through the DEPArray Nxt system (Menarini Silicon Biosystems), and individually partitioned. The cells then underwent lysis, DNA extraction, and whole genome amplification (WGA) using Menarini Silicon Biosystems' Ampli1 WGA kit. Cells that passed QC were ran through low-pass sequencing and processed through Menarini's MSBiosuites for CNV analysis. The validated workflow was then integrated with an antigen agnostic CTC isolation process, termed the Labyrinth, to process the blood of a pancreatic cancer patient. This workflow combines the benefits of label-free CTC isolation with single-cell genomic analysis.