Six-layer structure for genomics and its applications

Abstract

The term 'genetics' was coined before an understanding of DNA sequence data was achieved, and it is now insufficient to describe the broad areas in which DNA data have important roles. The term genomics is more broadly descriptive, but it does not provide a satisfactory conceptual framework that scientists can share. Here I propose a six-layer structure that describes the entire scientific field for 'genomics'. The proposed layers are 'life' as the uppermost layer, followed by 'species', 'population', 'family', 'individual' and finally 'cell' as the bottommost layer. In each pair of adjacent layers, each member of the upper layer comprises a set of members of the lower layer. In each layer, we can define consistent partial orders of members based on genomic data in the forms of phylogenic and pedigree trees. Although total orders such as those defined for time and space in physics cannot be defined in biology, defining consistent partial orders allows mathematical analysis to be performed. I will show that mathematical genetics studies can be understood as attempts to bridge gaps between layers of the proposed six-layer structure, while genetic tests can be understood as procedures to differentiate among members of each layer by using genomic data.