Genetic Variation and Gene Discovery

There has been remarkable progress in understanding genetic variation and its impact on human health. This chapter describes the variety of genomic technologies now available to advance our understanding of heritable diseases that afflict children. Sequencing of the whole genome or exome (targeted exome capture) by Next-Gen sequencing technology is becoming the standard in translational research to identify novel genetic variants that underlie risk of developing a disease. The process of analysis of raw data from Next-Gen sequencing is complex, computationally intensive, and uses many different software applications. Integrated sets of tools (software applications) are available to compare the DNA sequences of genes in an affected patient with the reference sequence of a normal control and with sequences of other patients with the same disease. Sites in the DNA are identified where there is statistical evidence for a rare or novel variant in the patient, including single or multi-nucleotide substitutions, insertions and deletions (indels), sequence rearrangements, and copy number variations. There can be considerable phenotypic variation among patients with defects in the same gene and conversely patients with similar phenotypes may or may not share variants in the same gene. There is also variation in types of changes in DNA sequences that can cause loss of function. Stratification of sequencing data at both the phenotypic and genotypic level is critical for effective discovery of sequence variants that cause disease. This chapter includes several illustrations of use of Next-Gen sequencing technology in genetics research.