How secondary findings are made

In this chapter, secondary findings are discussed in the context of exome and genome sequencing that is being conducted to identify genetic variation in individuals suspected to have genetic disease. We summarize how secondary findings are discovered in clinical large-scale DNA sequencing and the sequencing technologies that are currently being employed by clinical and research laboratories. Moreover, we detail the downstream analytical pipelines that are utilized to detect potentially medically relevant genetic variation and discuss places within this pipeline where secondary genetic findings can be proactively sought out or even avoided.