Clinical applications of next generation sequencing in cancer: From panels, to exomes, to genomes

This article will review recent impact of massively parallel next-generation sequencing (NGS) in our understanding and treatment of cancer. While whole exome sequencing (WES) remains popular and effective as a method of genetically profiling different cancers, advances in sequencing technology has enabled an increasing number of whole-genome based studies. Clinically, NGS has been used or is being developed for genetic screening, diagnostics, and clinical assessment. Though challenges remain, clinicians are in the early stages of using genetic data to make treatment decisions for cancer patients. As the integration of NGS in the study and treatment of cancer continues to mature, we believe that the field of cancer genomics will need to move towards more complete 100% genome sequencing. Current technologies and methods are largely limited to coding regions of the genome. A number of recent studies have demonstrated that mutations in non-coding regions may have direct tumorigenic effects or lead to genetic instability. Non-coding regions represent an important frontier in cancer genomics

Childhood tonsillectomy alters the primary distribution of HPV‐related oropharyngeal squamous cell carcinoma

ObjectivesWe investigated how tonsillectomy during childhood may influence the distribution of human papillomavirus (HPV) positive cancer of the tonsils in adult life using p16 as a surrogate marker for HPV infection.Study DesignRetrospective observational study.MethodsA total of 280 patients diagnosed with oropharyngeal squamous cell carcinoma (OPSCC) and known p16 status were eligible for this study. Each participant was called to obtain the childhood tonsillectomy history. Respondents were subgrouped by p16 status and the primary tumor location. Patient demographic and clinical information was analyzed for association with Fisher’s exact and Wilcoxon rank sum tests. Location of tumor was modeled using univariate (UVA) and multivariate (MVA) logistic regression with associated odds ratios (OR) and 95% confidence intervals.ResultsOf the 280 patients, 115 (41%) were respondents: 104 (90.4%) were p16 positive and 11 (9.6%) were p16 negative. For p16 positive patients, we observed a majority (93%) of intact tonsils in those with tonsil cancer, compared to 45% of intact tonsils in patients with p16 positive cancer elsewhere in the oropharynx (P < .001). MVA logistic regression showed that female gender (OR = 4.16, P = .0675), prior smoking history (OR = 2.6, P = .0367), and intact tonsils (OR = 15.2, P < .0001) were associated with tonsillar OPSCC.ConclusionWe found that patients with p16 positive OPSCC at a non‐tonsil site were much more likely to have had prior tonsillectomy vs those with p16 positive OPSCC arising within the tonsil. Nevertheless, we do not advocate tonsillectomies as a public health policy to reduce HPV‐related OPSCC.Level of Evidence6Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154902/1/lio2342_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154902/2/lio2342.pd