Genomic sequencing of rare diseases

Abstract Since the beginning of the Human Genome Project, sequencing of the human genome has driven the development of technologies and methods to discover the variation within it. While the cost of sequencing the original human haploid consensus reference genome was approximately $2.7 billion US dollars, the subsequent development of better and more efficient sequencing machines and methodologies, such as massively parallel next-generation sequencing technologies, dramatically reduced both the cost and time to sequence personal human genomes and apply these technologies for research and in the clinic. In addition, the development and refinement of targeted capture methods and reagents for exome sequencing resulted in a rapid increase in the number of human exomes sequenced and analyzed, dramatically expanding our knowledge of human coding variation. Concurrently, bioinformatic algorithms and tools have been developed to manage and analyze the tremendous amount of genomic data generated. This chapter aims to give an overview of the methodologies used to interrogate the human genome focusing mainly on genomic sequencing from Sanger sequencing to single-molecule DNA sequencing. Additionally, an overview of the analyses performed to identify medically relevant sequence variation and how these have been applied to successfully elucidate the molecular causes of rare diseases is provided. Finally, the application of genomic sequencing in the clinic and the limitations of the approach are discussed.