Duplex sequencing validation of PHLI-seq

Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to technical limitations. Here, we describe a novel approach, phenotype-based high-throughput laser-aided isolation and sequencing (PHLI-seq), which enables high-throughput isolation and genome-wide sequence analysis of single-cells or small numbers of cells to construct genomic maps within cancer tissue in relation to the images or phenotypes of the cells. By applying PHLI-seq, we reveal the heterogeneity of breast cancer tissues at a high-resolution and map the genomic landscape of the cells to their corresponding spatial locations and phenotypes in the 3D tumor mass.