title: The genomic landscape of polymorphic human nuclear mitochondrial insertions.
abstract: The transfer of mitochondrial genetic material into the nuclear genomes of eukaryotes is a well-established phenomenon that has been previously limited to the study of static reference genomes. The recent advancement of high throughput sequencing has enabled an expanded exploration into the diversity of polymorphic nuclear mitochondrial insertions (NumtS) within human populations. We have developed an approach to discover and genotype novel Numt insertions using whole genome, paired-end sequencing data. We have applied this method to a thousand individuals in 20 populations from the 1000 Genomes Project and other datasets and identified 141 new sites of Numt insertions, extending our current knowledge of existing NumtS by almost 20%. We find that recent Numt insertions are derived from throughout the mitochondrial genome, including the D-loop, and have integration biases that differ in some respects from previous studies on older, fixed NumtS in the reference genome. We determined the complete inserted sequence for a subset of these events and have identified a number of nearly full-length mitochondrial genome insertions into nuclear chromosomes. We further define their age and origin of insertion and present an analysis of their potential impact to ongoing studies of mitochondrial heteroplasmy and disease.
authors.affiliation: Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Gargi
authors.initials: G
authors.lastname: Dayama
authors.affiliation: Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Sarah B
authors.initials: SB
authors.lastname: Emery
authors.affiliation: Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Jeffrey M
authors.identifier: http://orcid.org/0000-0002-9631-1465
authors.initials: JM
authors.lastname: Kidd
authors.affiliation: Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA remills@umich.edu.
authors.forename: Ryan E
authors.identifier: http://orcid.org/0000-0003-3425-6998
authors.initials: RE
authors.lastname: Mills
mesh_terms: D002467:Cell Nucleus / Q000235:genetics*; D015894:Genome, Human; D054629:Genome, Mitochondrial; D023281:Genomics / Q000379:methods; D006801:Humans; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D011110:Polymorphism, Genetic