title: Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools.
abstract: DNA sequencing identifies common and rare genetic variants for association studies, but studies typically focus on variants in nuclear DNA and ignore the mitochondrial genome. In fact, analyzing variants in mitochondrial DNA (mtDNA) sequences presents special problems, which we resolve here with a general solution for the analysis of mtDNA in next-generation sequencing studies. The new program package comprises 1) an algorithm designed to identify mtDNA variants (i.e., homoplasmies and heteroplasmies), incorporating sequencing error rates at each base in a likelihood calculation and allowing allele fractions at a variant site to differ across individuals; and 2) an estimation of mtDNA copy number in a cell directly from whole-genome sequencing data. We also apply the methods to DNA sequence from lymphocytes of ~2,000 SardiNIA Project participants. As expected, mothers and offspring share all homoplasmies but a lesser proportion of heteroplasmies. Both homoplasmies and heteroplasmies show 5-fold higher transition/transversion ratios than variants in nuclear DNA. Also, heteroplasmy increases with age, though on average only ~1 heteroplasmy reaches the 4% level between ages 20 and 90. In addition, we find that mtDNA copy number averages ~110 copies/lymphocyte and is ~54% heritable, implying substantial genetic regulation of the level of mtDNA. Copy numbers also decrease modestly but significantly with age, and females on average have significantly more copies than males. The mtDNA copy numbers are significantly associated with waist circumference (p-value = 0.0031) and waist-hip ratio (p-value = 2.4×10-5), but not with body mass index, indicating an association with central fat distribution. To our knowledge, this is the largest population analysis to date of mtDNA dynamics, revealing the age-imposed increase in heteroplasmy, the relatively high heritability of copy number, and the association of copy number with metabolic traits.
authors.affiliation: Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, Maryland.
authors.forename: Jun
authors.initials: J
authors.lastname: Ding
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan; Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy; Università degli Studi di Sassari, Sassari, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Sidore
authors.affiliation: Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, Maryland.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Butler
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan.
authors.forename: Mary Kate
authors.initials: MK
authors.lastname: Wing
authors.affiliation: Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, Maryland.
authors.forename: Yong
authors.initials: Y
authors.lastname: Qian
authors.affiliation: Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, Maryland.
authors.forename: Osorio
authors.initials: O
authors.lastname: Meirelles
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan; Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Busonero
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan.
authors.forename: Lam C
authors.initials: LC
authors.lastname: Tsoi
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan; Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Maschio
authors.affiliation: Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Angius
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan.
authors.forename: Hyun Min
authors.initials: HM
authors.lastname: Kang
authors.affiliation: Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, Maryland.
authors.forename: Ramaiah
authors.initials: R
authors.lastname: Nagaraja
authors.affiliation: Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy; Università degli Studi di Sassari, Sassari, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Cucca
authors.affiliation: Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan.
authors.forename: Gonçalo R
authors.initials: GR
authors.lastname: Abecasis
authors.affiliation: Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, Maryland.
authors.forename: David
authors.initials: D
authors.lastname: Schlessinger
mesh_terms: D000375:Aging; D000465:Algorithms; D001483:Base Sequence; D050218:Body Fat Distribution; D015992:Body Mass Index; D056915:DNA Copy Number Variations / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D005260:Female; D018628:Gene Dosage / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008214:Lymphocytes / Q000166:cytology*; D008297:Male; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D009765:Obesity / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012737:Sex Factors; D055105:Waist Circumference / Q000235:genetics; D049629:Waist-Hip Ratio
chemical_list: D004272:DNA, Mitochondrial