Detecting and phasing minor single-nucleotide variants from long-read sequencing data.
Detecting and phasing minor single-nucleotide variants from long-read sequencing data.
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DOI：
10.1038/s41467-021-23289-4
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发表时间：
2021-05-24
影响因子：
16.6
通讯作者：
Schadt EE
中科院分区：
文献类型：
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作者：
Feng Z;Clemente JC;Wong B;Schadt EE
细胞遗传异质性在许多生物学状况中是常见的，包括癌症、微生物组和多种病原体的共感染。检测和定相微小变异在破译细胞遗传异质性方面发挥着重要作用，但由于技术限制，它们仍然是困难的任务。最近，包括Pacific Biosciences和Oxford Nanopore在内的长读段测序技术为应对这些挑战提供了机会。然而，高错误率使得很难充分利用这些技术。为了填补这一空白，我们引入了iGDA，这是一种开源工具，可以从原始长读段测序数据中准确检测和定相微小的单核苷酸变异（SNV），其频率低至0.2%。我们还证明，iGDA可以从长时间读取的宏基因组数据中准确地重建同一物种的密切相关菌株（分歧≥0.011%）的单倍型。细胞遗传异质性在各种生物条件下很常见，但长读段测序在这一领域的应用受到错误率的限制。在这里，作者介绍了iGDA，这是一种用于从长读取测序数据中检测和定相微小变异的工具，可以准确重建单倍型。
Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, and co-infection of multiple pathogens. Detecting and phasing minor variants play an instrumental role in deciphering cellular genetic heterogeneity, but they are still difficult tasks because of technological limitations. Recently, long-read sequencing technologies, including those by Pacific Biosciences and Oxford Nanopore, provide an opportunity to tackle these challenges. However, high error rates make it difficult to take full advantage of these technologies. To fill this gap, we introduce iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, from raw long-read sequencing data. We also demonstrate that iGDA can accurately reconstruct haplotypes in closely related strains of the same species (divergence ≥0.011%) from long-read metagenomic data. Cellular genetic heterogeneity is common across biological conditions, yet application of long-read sequencing to this subject is limited by error rates. Here, the authors present iGDA, a tool for detection and phasing of minor variants from long-read sequencing data, allowing accurate reconstruction of haplotypes.
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影响因子：
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使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
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通讯作者：
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