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Tumor heterogeneity presents a challenge for infer ring clonal evolution and driver gene identification.Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level.To perform our analyses, we first devised and validated a high-throughput whole-genome single-cell se quencing method using two lymphoblastoid cell line single cells.We then carried out whole-exome single-cell sequencing of 90 cells from a JAK2-negative myeloproliferative neoplasm patient.The sequencing data from 58 cells passed our quality control criteria, and these data indicated that this neoplasm represented a monoclonal evolution.