Chapter 6 - DNA Sequencing and Other Methods of Exonic and Genomic Analyses

Abstract

DNA sequencing technologies, and the application of these technologies for exploring molecular bases of diseases as well as for clinical sequencing, are reviewed in this chapter. The methods of DNA sequencing include: 1) the Maxam–Gilbert method; 2) the Sanger method; and 3) next-generation sequencing (NGS) technologies. In addition, other technologies including fluorescence in situ hybridization (FISH) analysis, microarray-based comparative genomic hybridization (array CGH) analysis, polymerase chain reaction (PCR)-based methods (quantitative PCR analysis, multiplex ligation-dependent probe amplification (MLPA) analysis, PCR fragment analysis, and repeat-primed PCR analysis), and Southern blot hybridization analysis are also used to analyze alterations of structures of DNA molecules. Among these, in particular, NGS technologies are currently revolutionizing the field of molecular genetics research of diseases. Comprehensive genome sequence analyses employing NGS technologies have demonstrated excellent competence to identify molecular bases of diseases with Mendelian-trait as well as those with complex trait. NGS technologies are also being increasingly applied for clinical sequencing to provide molecular diagnoses of diseases.