Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

Tumor heterogeneity presents a challenge for inferring 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 sequencing 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. We further identified essential thrombocythemia (ET)-related candidate mutations such as SESN2 and NTRK1, which may be involved in neoplasm progression. This pilot study allowed the initial characterization of the disease-related genetic architecture at the single-cell nucleotide level. Further, we established a single-cell sequencing method that opens the way for detailed analyses of a variety of tumor types, including those with high genetic complex between patients. º Building a new whole-genome SCS of high genome coverage, sensitivity, and specificity º Whole-exome SCS of a typical JAK2-negative myeloproliferative neoplasm patient º Depicting intratumoral genetics of the neoplasm at a single-cell nucleotide level º Provision of evidence for monoclonal evolution of the neoplasm A new high-throughput method based on non-PCR amplification allows whole-exome sequencing of single cells at the nucleotide level. Sequencing of 90 individual tumor cells from a JAK2-negative myeloproliferative neoplasm provides evidence for monoclonal evolution of the cancer.