10.1371/journal.pgen.1005306 Jun Ding Jun Ding Carlo Sidore Carlo Sidore Thomas J. Butler Thomas J. Butler Mary Kate Wing Mary Kate Wing Yong Qian Yong Qian Osorio Meirelles Osorio Meirelles Fabio Busonero Fabio Busonero Lam C. Tsoi Lam C. Tsoi Andrea Maschio Andrea Maschio Andrea Angius Andrea Angius Hyun Min Kang Hyun Min Kang Ramaiah Nagaraja Ramaiah Nagaraja Francesco Cucca Francesco Cucca Gonçalo R. Abecasis Gonçalo R. Abecasis David Schlessinger David Schlessinger Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools Public Library of Science 2015 association body mass index heteroplasmie Assessing Mitochondrial DNA Variation heteroplasmy homoplasmie mtDNA copy numbers copy number mtDNA copy number sequencing error rates Tailored Sequencing Analysis Tools DNA sequencing variant 2015-07-14 03:37:42 Dataset https://plos.figshare.com/articles/dataset/_Assessing_Mitochondrial_DNA_Variation_and_Copy_Number_in_Lymphocytes_of_2_000_Sardinians_Using_Tailored_Sequencing_Analysis_Tools_/1482884 <div><p>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<sup>-5</sup>), 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.</p></div>