Rapid diagnosis of genetic diseases is of great importance in neonatal medicine. Timely molecular diagnosis can improve the outcome of treatment or facilitate the decision to discontinue treatment. NGS technology is becoming increasingly important as a diagnostic tool for rapid and accurate diagnosis in neonatal medicine. The second- and third-generation NGS can be used for various analyses, including multigene panels, WES and WGS. Each of the NGS applications has its advantages and disadvantages, that are useful in different conditions. Of particular importance is the rWGS system, which allows molecular diagnosis in less than a day. The key to future development of such systems will be to create an efficient, automated and rapid bioinformatics analysis that can be performed on a large scale. NGS technology is also gradually gaining acceptance in neonatal screening, but the point at which it could independently replace biochemical testing is still a long way off. Advances in NGS technology raise new ethical issues related to informed consent and reporting of secondary findings. Practical answers to these questions must be found before technology can be used in clinical practise. A system of semi-quantitative metrics to assess clinical utility is offered as a potentially effective tool to address such ethical dilemmas.
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