High-throughput sequencing

Abstract High-throughput sequencing (HTS) has brought a paradigm shift in large-scale precision medicine initiatives. Recently, electronic health records have been integrated with HTS technologies to accrue genomic variants linked with disease phenotypes and generate patient specific reports with clinically actionable genomic variants. HTS innovations have drawn favorable clinical outcomes in cancer, monogenic, and syndromic conditions. In this scenario, HTS data analysis is going to be integral part, in the foreseeable future, for hospitals initiating genomics-guided therapeutic practice. Moreover, HTS analysis can identify the full spectrum of genetic variations, epigenetic changes, altered gene expressions, and gene fusions—both known and novel—with respect to disease phenotypes. Therefore, this chapter encompasses an overview of HTS data analysis protocols pertaining to genomics, transcriptomics, and epigenetic data. It also presents examples on raw data preprocessing/quality checking, DNA-seq analysis (whole exome) for short variants discovery and RNA-seq analysis to identify differentially expressed genes. The overview and examples would guide researchers/clinicians to identify genetic variants of clinical interest as well as potential biomarkers and drug targets of a disease. The examples dataset discussed in the chapter can also be accessed at www.genomics.icmr.org.in/htsdata/ .