Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools.
Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools.
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DOI：
10.1371/journal.pgen.1005306
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发表时间：
2015-07
期刊：
影响因子：
4.5
通讯作者：
Schlessinger D
中科院分区：
文献类型：
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作者：
Ding J;Sidore C;Butler TJ;Wing MK;Qian Y;Meirelles O;Busonero F;Tsoi LC;Maschio A;Angius A;Kang HM;Nagaraja R;Cucca F;Abecasis GR;Schlessinger D
DNA测序为关联研究确定了常见和罕见的遗传变异，但研究通常集中在核DNA的变异上，而忽略了线粒体基因组。事实上，分析线粒体DNA(MtDNA)序列的变异会带来特殊的问题，我们在这里用一个通用的解决方案来解决下一代测序研究中的mtDNA分析问题。新的程序包包括1)一种算法，旨在识别mtDNA变异(即同质和异质)，在似然计算中纳入每个碱基的测序错误率，并允许变异位置的等位基因比例因个体而异；以及2)直接从全基因组测序数据估计细胞中的mtDNA拷贝数。我们还将这些方法应用于约2,000名撒丁岛计划参与者的淋巴细胞DNA测序。正如预期的那样，母亲和后代共享所有的同质性，但异质性的比例较小。同质性和异质性都表现出比核DNA变异体高5倍的转换/颠换比率。此外，异质性随着年龄的增长而增加，尽管在20岁至90岁之间平均只有1种异质性达到4%的水平。此外，我们还发现线粒体DNA拷贝数平均为110拷贝/淋巴细胞，遗传性为54%，这意味着线粒体DNA水平受到实质性的遗传调控。随着年龄的增长，拷贝数也略有下降，但明显减少，女性的平均拷贝数明显多于男性。线粒体DNA拷贝数与腰围(p值=0.0031)和腰臀比(p值=2.4×10-5)显著相关，而与体重指数无关，提示与中心性脂肪分布有关。据我们所知，这是迄今为止对线粒体DNA动力学进行的最大规模的群体分析，揭示了异质性随年龄的增加，拷贝数的遗传力相对较高，以及拷贝数与代谢性状的关联。我们提出了一个新的程序，为线粒体DNA(线粒体中的小环状基因组，与细胞核中的DNA分离)的变异分析提供了一个通用的解决方案。这是必要的，因为许多大规模的基因研究正在使用新的DNA测序技术来帮助评估遗传变异及其对疾病的影响，但线粒体基因组经常被忽视，因为它存在于细胞中的许多副本中，使分析变得复杂。我们的方法既识别线粒体基因组上的变异，又估计mtDNA拷贝数。将这些程序应用于来自约2,000名撒丁岛项目参与者的DNA序列，我们发现异质性(在一个DNA位点具有多个等位基因的mtDNA变体)随着年龄的增长而增加，而且拷贝数具有相对较高的遗传性，并与代谢特征，特别是中央脂肪水平相关。该程序包可以促进从任何全基因组测序数据进行全面的mtDNA分析，增加对mtDNA动力学及其在衰老和新陈代谢中的潜在作用的了解。
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. We present a new program that provides a general solution for the analysis of variation of mtDNA (the small circular genome in mitochondria, separate from the DNA in the nucleus). This is needed because many large-scale genetic studies are using new DNA sequencing technologies to help assess genetic variation and its effects on disease, but the mitochondrial genome is often ignored because it exists in many copies in a cell, complicating analyses. Our approach both identifies variants on mitochondrial genome and estimates mtDNA copy number. Applying the programs to DNA sequence from ~2,000 SardiNIA project participants, we show that heteroplasmies (mtDNA variants with more than one allele at a DNA site) increase with age, and that copy number is relatively highly heritable and is correlated with metabolic traits, particularly central fat levels. The program package can facilitate comprehensive mtDNA analysis from any whole-genome sequencing data, with an increase in the understanding of mtDNA dynamics and its potential role in aging and metabolism.