Performance comparison of whole-genome sequencing platforms.
Performance comparison of whole-genome sequencing platforms.
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DOI：
10.1038/nbt.2065
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发表时间：
2011-12-18
影响因子：
46.9
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中科院分区：
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全基因组测序正变得越来越普遍，但Illumina和Complete Genomics最广泛使用的平台的变异识别的准确性和完整性尚未报道。在这里，我们用这两种技术对个体的基因组进行测序，平均覆盖率约为76×，并比较了它们在序列覆盖率和单核苷酸变异（SNV），插入和缺失（indels）的调用方面的性能。尽管约370万个独特SNV中有88.1%在平台之间是一致的，但仍有数万个平台特异性调用位于基因和其他基因组区域。相比之下，26.5%的indel在平台之间是一致的。靶富集验证了92.7%的一致SNV，而基因分型阵列的验证显示灵敏度为99.3%。验证实验还表明，>60%的平台特异性变体确实存在于基因组中。我们的研究结果对于理解基因组测序平台的准确性和完整性具有重要意义。
Whole-genome sequencing is becoming commonplace, but the accuracy and completeness of variant calling by the most widely used platforms from Illumina and Complete Genomics have not been reported. Here we sequenced the genome of an individual with both technologies to a high average coverage of ~76×, and compared their performance with respect to sequence coverage and calling of single-nucleotide variants (SNVs), insertions and deletions (indels). Although 88.1% of the ~3.7 million unique SNVs were concordant between platforms, there were tens of thousands of platform-specific calls located in genes and other genomic regions. In contrast, 26.5% of indels were concordant between platforms. Target enrichment validated 92.7% of the concordant SNVs, whereas validation by genotyping array revealed a sensitivity of 99.3%. The validation experiments also suggested that >60% of the platform-specific variants were indeed present in the genome. Our results have important implications for understanding the accuracy and completeness of the genome sequencing platforms.
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影响因子：
46.9
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通讯作者：
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影响因子：
3.7
作者：
Chen R;Davydov EV;Sirota M;Butte AJ
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Butte AJ
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通讯作者：
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