Box 1.

Definitions of terminology in precision medicine, genome sequencing, and cancer systems biology

Term	Definition
Precision medicine	Medical model tailored to the individual patient. Integrates research knowledge from biomarkers and genomic profiles to accomplish quick, efficient, and accurate medical predictions and decisions.
Big data	Data sets outsize traditional data management and processing. Scale, complexity, and dynamics require new architecture, techniques, algorithms, and analytics to manage it and extract value from it. Big data can be identified by V-type characteristics (see Table 1). Big data analysis can reveal trends, patterns, and correlations based on network interactions.
Genomics	Study of all genes in the human genome. Genomics aims at a full collection of genes and mutations, both inherited and somatic that contribute to the development of an organism, as well as its normal homeostatic function or diseased states. Genome is a portmanteau of the words gene and chromosome.
Epigenomics	Chemical modifications that do not change the DNA sequence but can affect gene activity. Epigenomics refers to capturing epigenetic marks on a genome-wide scale, such as DNA methylation and post-translational modifications of histone chromatin, while epigenetics focuses on regulatory factors and reversible processes affecting gene expression, non-genomic inheritance, and phenotypes that are not the result of variations in DNA sequence.
Systems biology	Science of quantifying, modeling, and visualizing network interactions. Once a model is formulated, systems biology cycles between testable hypotheses and experimental validation.
Genome sequencing	Collection of methods to sequence an entire genome in a single run. The technology involves the capture of fragmented genomic DNA by oligonucleotide probes that collectively cover all exonic or whole genomic sequence regions (abbreviated as WES or WGS, respectively).
Genotyping	The process of determining the genetic makeup of an individual. This can include an entire genome or be targeted to regions associated with a clinical phenotype.
SNP	Variation at a single position in a DNA sequence among individuals or chromosomes. If more than 1% of a population does not carry the same nucleotide at a specific position in the DNA sequence, then this variation can be classified as a single-nucleotide polymorphism, abbreviated SNP and pronounced as snip. SNPs are not just associated with genes or diseases; they can also occur in non-annotated regions of DNA.
SCNA	Somatic copy number alterations, abbreviated SCNAs, are multiplications of deletions of chromosome arms of focal regions that have arisen in a non-germline tissue for example just in a tumor. In contrast, copy number variations, abbreviated CNVs, originate from changes in germline cells and are thus in all cells of the organism.
Master regulator	Rate-limiting step positioned at top of hierarchy. Topologically, master regulators are found at branch points of networks influencing metabolic flux or signaling pathways related to cellular decisions on proliferation, survival, or differentiation.
MAPK pathway	Chain of signaling molecules that communicates a signal from a cell surface receptor into the nucleus of the cell to control a gene expression program including proliferation, mitosis, differentiation, and cell survival. A mitogen-activated protein kinase, abbreviated as MAP kinase or MAPK is part of a kinase family specific to phosphorylation of amino acids serine, threonine, and tyrosine. MAPKs are operated as switches in an amplifying cascade, where phosphorylation of one kinase results in activation of the next kinase. Oncogenic mutations can result in constitutively activated kinases, thereby triggering uncontrolled cell proliferation. Major pathway that is dysregulated in malignant melanoma.
Immunotherapy	Engages certain parts of a person’s immune system to fight diseases such as cancer. This can be accomplished by antibodies, vaccines, or stimulation of the immune system. Immune evasion is a hiding mechanism of cancer cells, which manage to downregulate surface markers that can be recognized by the immune system thereby facilitating unmonitored survival. T-cell immune checkpoint inhibitors silence control elements of the immune system and result in enhanced immune recognition and attack of cancer cells.
Neoantigen	Newly formed epitope that has not been previously recognized by the immune system. New epitopes can arise as a consequence of tumor-specific mutations. Based on such epitopes, the immune system can respond or suppress tumor-reactive T-cell populations, thereby playing a major factor in the activity of immunotherapies such as T-cell checkpoint blockade and adoptive T-cell therapy.
Oncometabolite	Small molecule whose accumulation leads to cancer initiation and progression by metabolic and signaling dysregulation. Specific enantiomers of hydroxy-keto acids or amino acids are accumulated as a result of defective enzymes in cancer and cause genome-wide changes of gene expression by acting as inhibitors of regulatory proteins.