that should occur prior to use to direct treatment choice in a clinical trial. In this chapter, the discovery phase (see Figures 2-1 and S-1) of the recommended omics-based test development process is discussed, beginning with examples of specific types of omics studies and the technologies involved, followed by the statistical, computational, and bioinformatics challenges that arise in the analysis of omics data. Some of these challenges are unique to omics data, whereas others relate to fundamental principles of good scientific research. The chapter begins with an overview of the types of omics data and a discussion of emerging directions for omics research as they relate to the discovery and future development of omics-based tests for clinical use.
Examples of the types of omics data that can be used to develop an omics-based test are discussed below. This list is by no means meant to be comprehensive, and indeed a comprehensive list would be impossible because new omics technologies are rapidly developing.
The genome is the complete sequence of DNA in a cell or organism. This genetic material may be found in the cell nucleus or in other organelles, such as mitochondria. With the exception of mutations and chromosomal rearrangements, the genome of an organism remains essentially constant over time. Complete or partial DNA sequence can be assayed using various experimental platforms, including single nucleotide polymorphism (SNP) chips and DNA sequencing technology. SNP chips are arrays of thousands of oligonucleotide probes that hybridize (or bind) to specific DNA sequences in which nucleotide variants are known to occur. Only known sequence variants can be assayed using SNP chips, and in practice only common variants are assayed in this way. Genomic analysis also can detect insertions and deletions and copy number variation, referring to loss of or amplification of the expected two copies of each gene (one from the mother and one from the father at each gene locus). Personal genome sequencing is a more recent and powerful technology, which allows for direct and complete sequencing of genomes and transcriptomes (see below). DNA also can be modified by methylation of cytosines (see Epigenomics, below). There is also an emerging interest in using genomics technologies to study the impact of an individual’s microbiome (the aggregate of microorganisms that reside within the human body) in health and disease (Honda and Littman, 2011; Kinros et al., 2011; Tilg and Kaser, 2011).