title: High-throughput sequencing in mitochondrial DNA research.
abstract: Next-generation sequencing, also known as high-throughput sequencing, has greatly enhanced researchers' ability to conduct biomedical research on all levels. Mitochondrial research has also benefitted greatly from high-throughput sequencing; sequencing technology now allows for screening of all 16,569 base pairs of the mitochondrial genome simultaneously for SNPs and low level heteroplasmy and, in some cases, the estimation of mitochondrial DNA copy number. It is important to realize the full potential of high-throughput sequencing for the advancement of mitochondrial research. To this end, we review how high-throughput sequencing has impacted mitochondrial research in the categories of SNPs, low level heteroplasmy, copy number, and structural variants. We also discuss the different types of mitochondrial DNA sequencing and their pros and cons. Based on previous studies conducted by various groups, we provide strategies for processing mitochondrial DNA sequencing data, including assembly, variant calling, and quality control.
authors.affiliation: Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: Ye
authors.affiliation: Center for Human Genetics, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Samuels
authors.affiliation: Vanderbilt Technology for Advanced Genomics, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Travis
authors.initials: T
authors.lastname: Clark
authors.affiliation: Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Guo
mesh_terms: D056915:DNA Copy Number Variations; D004272:DNA, Mitochondrial / Q000737:chemistry* / Q000235:genetics*; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D028361:Mitochondrial Diseases / Q000175:diagnosis; D020641:Polymorphism, Single Nucleotide
chemical_list: D004272:DNA, Mitochondrial
keywords: Copy number; Heteroplasmy; High throughput sequencing; Mutation; Next generation sequencing; SNP