title: Intra-tumor genetic heterogeneity and mortality in head and neck cancer: analysis of data from the Cancer Genome Atlas.
abstract: BACKGROUND
  Although the involvement of intra-tumor genetic heterogeneity in tumor progression, treatment resistance, and metastasis is established, genetic heterogeneity is seldom examined in clinical trials or practice. Many studies of heterogeneity have had prespecified markers for tumor subpopulations, limiting their generalizability, or have involved massive efforts such as separate analysis of hundreds of individual cells, limiting their clinical use. We recently developed a general measure of intra-tumor genetic heterogeneity based on whole-exome sequencing (WES) of bulk tumor DNA, called mutant-allele tumor heterogeneity (MATH). Here, we examine data collected as part of a large, multi-institutional study to validate this measure and determine whether intra-tumor heterogeneity is itself related to mortality.
  
  
  RESULTS
  Clinical and WES data were obtained from The Cancer Genome Atlas in October 2013 for 305 patients with head and neck squamous cell carcinoma (HNSCC), from 14 institutions. Initial pathologic diagnoses were between 1992 and 2011 (median, 2008). Median time to death for 131 deceased patients was 14 mo; median follow-up of living patients was 22 mo. Tumor MATH values were calculated from WES results. Despite the multiple head and neck tumor subsites and the variety of treatments, we found in this retrospective analysis a substantial relation of high MATH values to decreased overall survival (Cox proportional hazards analysis: hazard ratio for high/low heterogeneity, 2.2; 95% CI 1.4 to 3.3). This relation of intra-tumor heterogeneity to survival was not due to intra-tumor heterogeneity's associations with other clinical or molecular characteristics, including age, human papillomavirus status, tumor grade and TP53 mutation, and N classification. MATH improved prognostication over that provided by traditional clinical and molecular characteristics, maintained a significant relation to survival in multivariate analyses, and distinguished outcomes among patients having oral-cavity or laryngeal cancers even when standard disease staging was taken into account. Prospective studies, however, will be required before MATH can be used prognostically in clinical trials or practice. Such studies will need to examine homogeneously treated HNSCC at specific head and neck subsites, and determine the influence of cancer therapy on MATH values. Analysis of MATH and outcome in human-papillomavirus-positive oropharyngeal squamous cell carcinoma is particularly needed.
  
  
  CONCLUSIONS
  To our knowledge this study is the first to combine data from hundreds of patients, treated at multiple institutions, to document a relation between intra-tumor heterogeneity and overall survival in any type of cancer. We suggest applying the simply calculated MATH metric of heterogeneity to prospective studies of HNSCC and other tumor types.
authors: Center for Cancer Research and Division of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, United States of America.
authors: Edmund A
authors: EA
authors: Mroz
authors: Aaron D
authors: AD
authors: Tward
authors: Department of Otology and Laryngology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America; The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
authors: Aaron M
authors: AM
authors: Tward
authors: Department of Otology and Laryngology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America.
authors: Rebecca J
authors: RJ
authors: Hammon
authors: Department of Otology and Laryngology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America.
authors: Yin
authors: Y
authors: Ren
authors: Center for Cancer Research and Division of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, United States of America; Department of Otology and Laryngology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America; Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, Ohio, United States of America.
authors: James W
authors: JW
authors: Rocco
mesh_terms: D000368:Aged; D000483:Alleles; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000821:virology; D004273:DNA, Neoplasm / Q000032:analysis*; D059472:Exome; D005260:Female; D014644:Genetic Variation; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000401:mortality; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009959:Oropharyngeal Neoplasms / Q000235:genetics / Q000821:virology; D027383:Papillomaviridae; D016016:Proportional Hazards Models; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA
chemical_list: D004273:DNA, Neoplasm