Translating Next-Generation-Sequencing into Precision Medicine
Next-Generation Sequencing (NGS) was initially used as an experimental method in exploratory research and in the search for novel scientific insights. In precision medicine additional critera apply, for example the testing method must answer specific clinical questions, while being subject to stringent standards of economy, liability and reproducibility. In accredited clinical NGS testing, laboratories must now increasingly document their standard procedures for computational validation (in silico validation) of NGS results. In this dissertation I describe possible in silico validation procedures based on my publications on the Backmapping method and on the pibase and Vy-PER software tools. These procedures take into account potential sources of errors from the biology itself, the lab methods, and bioinformatic methods. My pibase publication A deals with the validation of individual single nucleotide substitutions and the systematic elimination of error sources. My Backmapping publication B looks at potential artifacts that are based on biological sequence similarity between different regions of the human genome. These similarities may or may not lead to bioinformatic ambiguities when sequences are aligned to a reference genome. In consequence, potential artifacts may crop up which may only be exposed with the help of alternative genomic references and alternative alignment methods. My Vy-PER publication C presents an improved method to detect patient-individual virus genome particle integrations into the patient’s genome and to eliminate artifacts.