Sequence-specific error profile of Illumina sequencers.
Sequence-specific error profile of Illumina sequencers.
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DOI：
10.1093/nar/gkr344
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发表时间：
2011-07
影响因子：
14.9
通讯作者：
Kanaya S
中科院分区：
文献类型：
--
作者：
Nakamura K;Oshima T;Morimoto T;Ikeda S;Yoshikawa H;Shiwa Y;Ishikawa S;Linak MC;Hirai A;Takahashi H;Altaf-Ul-Amin M;Ogasawara N;Kanaya S
我们在从Illumina基因组分析仪（GA）获得的读数的映射中鉴定了连续错误调用的序列特异性起始位置。对错误识别模式的详细分析表明，潜在的机制涉及测序过程中碱基延伸过程的序列特异性干扰。触发这种序列特异性错误（SSE）的两种主要序列模式是：（i）反向重复序列和（ii）GGC序列。我们推测，这些序列有利于通过抑制单碱基延伸，通过：（i）折叠单链DNA和（ii）改变酶的偏好。这种现象是序列覆盖率变异性和群体靶向方法（如RNA-seq和ChIP-seq）观察到的不利偏倚的主要原因。此外，SSE是错误的单核苷酸多态性（SNP）调用的潜在原因，也显着阻碍从头组装。本文强调了认识SSE及其潜在机制的重要性，希望提高Illumina测序仪的潜在实用性。
We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers.
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