Chapter 12 - Bioinformatics resources, databases, and tools for human mtDNA

Abstract

The topic of this chapter owes a lot to the work of Sanger first, and Maxam and Gilbert, thereafter. They designed and implemented the techniques that allow us to produce the sequence of nucleotides that make up any piece of DNA. With the advent of sequencing technologies, it was immediately clear that the explosion of data that would be produced would require the design and implementation of databases in which to store data, as well as the setting up of systems for querying sequences, extracting, and analyzing them. In this scenario, the first nucleus of nucleotide sequences produced and stored in public nucleotide databases also included the first complete human mitochondrial genome, sequenced in 1981: the so called “Cambridge Reference Sequence” then revised as rCRS and since then universally adopted as a reference sequence for both population and clinical studies. In more recent times, a virtual sequence has been produced with the aim of better simulating the process of generations of world populations namely the “Reconstructed Sapiens Reference Sequence”. Overall, a great number of complete human mitochondrial genomes or fragments regarding the major control region D-loop have been sequenced since then starting from the representative samples of different populations within mtDNA phylogeny studies as well as samples collected within forensic analyses and clinical research. Because of the range of mtDNA variants with potential clinical and evolutionary relevance, difficulties can be encountered in deciding whether or not a particular mtDNA variant is relevant for either clinical or evolutionary arguments. This choice is guided by the four generally accepted canonical criteria, that is (1) knowledge about the neutral nature of a polymorphism, (2) the functional effect in a conserved site, (3) the heteroplasmic level, and (4) the association of this latter to the severity of clinical symptoms observed. Bioinformatics resources and tools have been developed to manage and analyze this enormous volume of information, with the aim of annotating and classifying genomes and variants. In this chapter, we provide a comprehensive overview of the concepts underlying the criteria to assess mitochondrial variant pathogenicity, as well as bioinformatics databases and tools.