Single-Nucleotide Polymorphisms: An Overview of the Sequence Polymorphisms

Single nucleotide polymorphisms (SNPs), that is, substitutions or insertions/deletions of a single nucleotide, are the most common variants in the human genomes. Because of their low mutation rate, they are mostly biallelic and evolutionary stable and a higher number of SNPs is required to have a discrimination capacity similar to microsatellites. Nonetheless, these markers can have several applications in forensic genetics, for example, as ancestry informative markers. Due to their importance, in this chapter we will explore the main molecular mechanisms leading to the onset of new SNPs (namely, spontaneous mutations, induced mutations, and gene conversion) and the de novo mutation rate in the human genome. We will also consider two main aspects of the de novo mutation rate: (1) the paternal age effect, that is, the increase of the mutation rate in offspring of elderly fathers and (2) the presence in the genome of hyper-mutational sites such as the CpG dinucleotides. Finally, we will explore the possible use of SNPs as analysis tools, taking as an example the human Y chromosome, which represents an interesting case because of its haploidy and paternal inheritance pattern.