A study published in Nature (2011) describes the use of single-cell sequencing to infer tumor evolution. Researchers used flow-sorted nuclei, whole genome amplification, and next-generation sequencing to analyze genomic copy number in individual cells. They applied this method to two breast cancer cases, revealing three distinct clonal subpopulations in a polygenomic tumor and a single clonal expansion in a monogenomic primary tumor and its liver metastasis. They also identified an abundant subpopulation of genetically diverse 'pseudodiploid' cells that do not travel to metastatic sites. These findings suggest that tumors grow through punctuated clonal expansions rather than gradual progression. The study used single nucleus sequencing (SNS) to isolate nuclei and amplify DNA for sequencing. They developed methods to analyze copy number using variable-length bins, which corrected for biases in whole genome amplification. They validated their method by comparing single-cell and bulk DNA profiles, finding high correlation between them. They also analyzed tumor substructures using neighbor-joining trees and identified common breakpoints to build phylogenetic trees. The study found that primary tumors originated from a single clonal expansion and that metastatic cells likely arose from this expansion with minimal further evolution. Pseudodiploid cells showed remarkable genomic heterogeneity and did not undergo clonal expansions. The findings suggest that primary and metastatic tumors have distinct copy number profiles, with differences in the degree of copy number change rather than breakpoints. The study also showed that pseudodiploid cells are a significant portion of diploid cells in tumors, indicating they may emerge from an ongoing process generating genomic diversity. The results support the idea that metastatic cells arise late in tumor development, consistent with previous findings using bulk DNA. The study highlights the importance of single-cell analysis in understanding tumor evolution and the potential of SNS to identify previously undetectable cell types. The findings suggest that tumor evolution is characterized by punctuated clonal expansions, with few persistent intermediates.A study published in Nature (2011) describes the use of single-cell sequencing to infer tumor evolution. Researchers used flow-sorted nuclei, whole genome amplification, and next-generation sequencing to analyze genomic copy number in individual cells. They applied this method to two breast cancer cases, revealing three distinct clonal subpopulations in a polygenomic tumor and a single clonal expansion in a monogenomic primary tumor and its liver metastasis. They also identified an abundant subpopulation of genetically diverse 'pseudodiploid' cells that do not travel to metastatic sites. These findings suggest that tumors grow through punctuated clonal expansions rather than gradual progression. The study used single nucleus sequencing (SNS) to isolate nuclei and amplify DNA for sequencing. They developed methods to analyze copy number using variable-length bins, which corrected for biases in whole genome amplification. They validated their method by comparing single-cell and bulk DNA profiles, finding high correlation between them. They also analyzed tumor substructures using neighbor-joining trees and identified common breakpoints to build phylogenetic trees. The study found that primary tumors originated from a single clonal expansion and that metastatic cells likely arose from this expansion with minimal further evolution. Pseudodiploid cells showed remarkable genomic heterogeneity and did not undergo clonal expansions. The findings suggest that primary and metastatic tumors have distinct copy number profiles, with differences in the degree of copy number change rather than breakpoints. The study also showed that pseudodiploid cells are a significant portion of diploid cells in tumors, indicating they may emerge from an ongoing process generating genomic diversity. The results support the idea that metastatic cells arise late in tumor development, consistent with previous findings using bulk DNA. The study highlights the importance of single-cell analysis in understanding tumor evolution and the potential of SNS to identify previously undetectable cell types. The findings suggest that tumor evolution is characterized by punctuated clonal expansions, with few persistent intermediates.