Validation of Microarray-Based Resequencing of 93 Worldwide Mitochondrial Genomes
Validation of Microarray-Based Resequencing of 93 Worldwide Mitochondrial Genomes
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DOI：
10.1002/humu.20816
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发表时间：
2009-01-01
期刊：
影响因子：
3.9
通讯作者：
Oefner, Peter J.
中科院分区：
文献类型：
--
作者：
Hartmann, Anne;Thieme, Marian;Oefner, Peter J.
人类线粒体基因组由 16,569 个碱基对的多拷贝环状 dsDNA 分子组成。它编码 13 种蛋白质、两种核糖体基因和 22 种 tRNA，这些对于真核细胞中通过氧化磷酸化产生细胞 ATP 至关重要。线粒体DNA (mtDNA) 的种系突变是母系遗传疾病的重要原因，而体细胞mtDNA 突变可能在衰老和癌症中发挥重要作用。 mtDNA多态性，isms也广泛应用于群体和法医遗传学。因此，能够快速、廉价且准确地对 mtDNA 进行测序的方法引起了人们的极大兴趣。一种这样的方法是Affymetrix GeneChip 人类线粒体重测序阵列2.0(MitoChip v.2.0)(Santa Clara，CA)。通过 MitoChip 和双脱氧终止子测序对全球 93 个线粒体基因组进行直接比较，结果显示 MitoChip 的平均检出率为 99.48%，准确度 >= 99.98%。良好的性能是通过使用内部软件对阵列上的附加探针进行自动分析而实现的，这些探针涵盖了高变区（HVR）中最常见的单倍型。未能识别碱基主要与存在 >= 4C 碱基或该碱基上游或下游 12 个碱基内的序列变体有关。 MitoChip 的一个主要缺点是它无法检测插入/缺失以及异质性检测的灵敏度和特异性较低。然而，mtDNA 系统发育中绝大多数定义多态性的单倍群都可以比传统测序更明确、更快速地调用。
The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorph, isms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip(R) Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of >= 99.98% for the MitoChip. The good performance was achieved by using in,house software for the auitomated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of >= 4C bases or a sequence variant within 12 bases up or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could he called unambiguously and more rapidly than with conventional sequencing.