Chapter One

Zhanjiang (John) Liu

Genetic Variations at the Genomic Level

The genome compositions of each individual of the same species are similar but different at the level of DNA sequences and its encoding capacity (sometimes in terms of what genes are transcribed, but perhaps more often in terms of how much the gene products are made), and thereby have different transcriptional activities, encoding similar but different proteins, or encoding same or similar proteins in different quantities, leading to different biological characteristics and performance. Upon comparison of the genomes of individuals within a population with their reference genome sequence of the species, several general types of genetic variations can be found (Figure 1.1): (1) a deletion due to the loss of one or more of bases; (2) insertion due to gain of one or more bases; (3) base substitution at various positions; (4) inversion of a DNA segment in its orientation; (5) rearrangements of multiple DNA segments within a both small and larger scope of the genome; and (6) copy number variation (CNV) due to insertions, deletions, and duplication or multiplication of a DNA segment(s). A deletion mutation and an insertion mutation can be viewed as the same phenomenon depending on what is used as the reference. Deletions/insertions in random genomic locations probably do not have much impact to its biological activities except when deletion/insertion happens within a gene or within its regulatory elements. Insertion/deletion of single base or two bases within a protein coding sequence would cause fr