A fundamental prerequisite for the efficacy of cancer immunotherapy is the presence of
functional, antigen-specific T cells within the tumor. Neoantigen-directed therapy is a …

Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer
evolution studies, providing insight into the clonality and relative ordering of mutations and …

Esophageal adenocarcinoma (EAC) incidence is increasing while 5-year survival rates
remain less than 15%. A lack of experimental models has hampered progress. We have …

Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of
how this genetic diversity emerges over time remains limited. A central challenge in studying …

Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic
mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome …

The sensitivity of massively-parallel sequencing has confirmed that most cancers are
oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine …

Cancer is a somatic evolutionary process characterized by the accumulation of mutations,
which contribute to tumor growth, clinical progression, immune escape, and drug resistance …

Rapid advances in high-throughput sequencing and a growing realization of the importance
of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies …

Understanding the mutational heterogeneity within tumors is a keystone for the development
of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to …

Cancer is a disease driven by evolutionary selection on somatic genetic and epigenetic
alterations. Here, we propose Canopy, a method for inferring the evolutionary phylogeny of …