Detecting Heteroplasmy from High-Throughput Sequencing of Complete Human Mitochondrial DNA Genomes
Detecting Heteroplasmy from High-Throughput Sequencing of Complete Human Mitochondrial DNA Genomes
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DOI：
10.1016/j.ajhg.2010.07.014
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发表时间：
2010-08-13
影响因子：
9.8
通讯作者：
Stoneking, Mark
中科院分区：
文献类型：
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作者：
Li, Mingkun;Schoenberg, Anna;Stoneking, Mark
异质性，即个体内存在多种mtDNA类型，以前主要通过使用间接方法检测，主要集中在控制区的高变片段上。下一代测序技术应该能够以更高的分辨率研究整个mtDNA基因组的异质性，因为每个位置都会产生许多独立的读数。然而，必须考虑与这些技术相关的较高错误率，以避免异质性的错误检测。我们使用模拟和phiX174序列数据来设计使用Illumina Genome Analyzer平台准确检测异质性的标准，并且我们使用人工混合物和重复数据来测试和完善标准。然后，我们将这些标准应用于通过平行标记方法生成的来自5个欧亚人群的131个个体的mtDNA序列读数。我们在32个个体的34个位点以10%或更高的频率鉴定了37种异质性。在同一个体中异质性突变和多态性之间的突变谱没有差异，但异质性突变的相对突变率显著高于人类mtDNA基因组中所有突变位点的估计值。此外，与来自相同个体的多态性数据相比，在异质性中观察到的非同义突变也显著过量。突变漂移和负选择都影响异质性的命运，以确定人类的多态性谱。通过适当的标准来避免由于测序错误而导致的假阳性，下一代技术可以为mtDNA异质性的全基因组方面提供新的见解。
Heteroplasmy, the existence of multiple mtDNA types within an individual, has been previously detected by using mostly indirect methods and focusing largely on just the hypervariable segments of the control region. Next-generation sequencing technologies should enable studies of heteroplasmy across the entire mtDNA genome at much higher resolution, because many independent reads are generated for each position. However, the higher error rate associated with these technologies must be taken into consideration to avoid false detection of heteroplasmy. We used simulations and phiX174 sequence data to design criteria for accurate detection of heteroplasmy with the Illumina Genome Analyzer platform, and we used artificial mixtures and replicate data to test and refine the criteria. We then applied these criteria to mtDNA sequence reads for 131 individuals from five Eurasian populations that had been generated via a parallel tagged approach. We identified 37 heteroplasmies at 10% frequency or higher at 34 sites in 32 individuals. The mutational spectrum does not differ between heteroplasmic mutations and polymorphisms in the same individuals, but the relative mutation rate at heteroplasmic mutations is significantly higher than that estimated for all mutable sites in the human mtDNA genome. Moreover, there is also a significant excess of nonsynonymous mutations observed among heteroplasmies, compared to polymorphism data from the same individuals. Both mutation-drift and negative selection influence the fate of heteroplasmies to determine the polymorphism spectrum in humans. With appropriate criteria for avoiding false positives due to sequencing errors, next-generation technologies can provide novel insights into genome-wide aspects of mtDNA heteroplasmy.