Next Generation Sequencing in the Context of Current Clinical Practice: Implementation and Challenges

Abstract

In the era of personalized medicine next generation sequencing (NGS) of normal and/or tumor DNA has already proven its value in the discovery phase of novel molecular defects associated with human disease. Different levels of information can be obtained from transcriptome sequencing, whole genome sequencing, exome sequencing, and sequencing of DNA enriched for methylated DNA. It is expected by many that soon the NGS sequencing will take its place in current clinical practice giving diagnostic, prognostic or predictive information. The complex biology underlying human disease is however now more and more surfacing. Already from the relatively simple tests using single biomarker sets, but now also from the discovery phase NGS reports, it became clear that tumor heterogeneity is a major issue in clinical practice. Although some advocate that the solution should be to screen all metastasized lesions, obtaining those will be burdensome for patients. How to use such knowledge on heterogeneous DNA alterations in metastatic lesions for clinical decision making is also not so easily answered. In current clinical practice we see that with the success of neo-adjuvant therapies for rectum-, esophagus-, stomach and breast cancers much of the molecular analyses should be done on limited material. With innovative methods, such as ultrasound guided trans-bronchial or trans- esophageal needle aspiration for staging of lung cancer combined with molecular analysis on very limited amounts of cancer cells, a similar trend can be seen. Although technical advances coming from e.g. single cell sequencing efforts can be applied it should be realized that such approaches can lead to diagnostic errors in true clinical practice. Therefore major quality assurance programs should be initiated before NGS can truly take its predicted role.