This study investigates the clonal and mutational evolution of primary triple-negative breast cancers (TNBCs), a subtype of breast cancer lacking estrogen receptor, progesterone receptor, and ERBB2 amplification, accounting for about 16% of all breast cancers. Using next-generation sequencing, the researchers analyzed 104 TNBC cases and found a wide spectrum of genomic evolution, with some cancers having only a few mutations and others containing hundreds. They used RNA sequencing to determine that only about 36% of mutations are expressed. Deep resequencing of 2,414 somatic mutations revealed the relative abundance of clonal frequencies among cases. TNBCs showed variation in clonal frequencies, with the basal subtype showing more variation than non-basal TNBCs. Mutations in p53, PIK3CA, and PTEN were clonally dominant, but in some tumors, their clonal frequencies were incompatible with founder status. Mutations in cytoskeletal and motility proteins occurred at lower clonal frequencies, suggesting they occurred later in tumor progression. The study also identified recurrent mutations in genes such as PARK2, PIK3CA, and BRCA2, and found that mutations in cytoskeletal genes were acquired later. The researchers also integrated CNA and mutation data with expression data to reveal genomic events associated with extreme changes in gene expression. They found that pathways involving p53 and PIK3CA showed significantly skewed distributions towards higher clonal frequencies, consistent with their roles in early tumorigenesis. The study highlights the clonal heterogeneity of TNBCs, with some patients' tumors showing few mutations and others showing extensive mutation burdens. The findings suggest that TNBCs are mutationally heterogeneous from the outset, with some patients' tumors having a small number of implicated pathways and few mutations, while others have extensive mutation burdens and multiple pathway involvement. The study also shows that the clonal composition of primary TNBCs is varied, with some cases showing only one or two frequency modes and others showing multiple. The results indicate that TNBCs already display a wide variation in clonal evolution at diagnosis, which mirrors the variation in mutational evolution. The study emphasizes the importance of understanding the clonal genotypes of individual tumors for developing effective therapies. The methods involved profiling the genomes and transcriptomes of 104 TNBCs using Affymetrix SNP6.0 arrays, RNA-seq, and whole exome/genome sequencing. The data were analyzed to detect somatic SNVs, indels, copy number alterations, gene fusions, and gene expression patterns. Mutations were validated using targeted ultra-deep amplicon sequencing and a statistical approach to determine single genes under selection. The study provides insights into the molecular mechanisms underlying TNBC progression and highlights the need for personalized approaches to treatment.This study investigates the clonal and mutational evolution of primary triple-negative breast cancers (TNBCs), a subtype of breast cancer lacking estrogen receptor, progesterone receptor, and ERBB2 amplification, accounting for about 16% of all breast cancers. Using next-generation sequencing, the researchers analyzed 104 TNBC cases and found a wide spectrum of genomic evolution, with some cancers having only a few mutations and others containing hundreds. They used RNA sequencing to determine that only about 36% of mutations are expressed. Deep resequencing of 2,414 somatic mutations revealed the relative abundance of clonal frequencies among cases. TNBCs showed variation in clonal frequencies, with the basal subtype showing more variation than non-basal TNBCs. Mutations in p53, PIK3CA, and PTEN were clonally dominant, but in some tumors, their clonal frequencies were incompatible with founder status. Mutations in cytoskeletal and motility proteins occurred at lower clonal frequencies, suggesting they occurred later in tumor progression. The study also identified recurrent mutations in genes such as PARK2, PIK3CA, and BRCA2, and found that mutations in cytoskeletal genes were acquired later. The researchers also integrated CNA and mutation data with expression data to reveal genomic events associated with extreme changes in gene expression. They found that pathways involving p53 and PIK3CA showed significantly skewed distributions towards higher clonal frequencies, consistent with their roles in early tumorigenesis. The study highlights the clonal heterogeneity of TNBCs, with some patients' tumors showing few mutations and others showing extensive mutation burdens. The findings suggest that TNBCs are mutationally heterogeneous from the outset, with some patients' tumors having a small number of implicated pathways and few mutations, while others have extensive mutation burdens and multiple pathway involvement. The study also shows that the clonal composition of primary TNBCs is varied, with some cases showing only one or two frequency modes and others showing multiple. The results indicate that TNBCs already display a wide variation in clonal evolution at diagnosis, which mirrors the variation in mutational evolution. The study emphasizes the importance of understanding the clonal genotypes of individual tumors for developing effective therapies. The methods involved profiling the genomes and transcriptomes of 104 TNBCs using Affymetrix SNP6.0 arrays, RNA-seq, and whole exome/genome sequencing. The data were analyzed to detect somatic SNVs, indels, copy number alterations, gene fusions, and gene expression patterns. Mutations were validated using targeted ultra-deep amplicon sequencing and a statistical approach to determine single genes under selection. The study provides insights into the molecular mechanisms underlying TNBC progression and highlights the need for personalized approaches to treatment.