HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints
HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints
复制标题
用于DNA存储的HEDGES纠错码可纠正indel并允许序列约束
DOI：
10.1073/pnas.2004821117
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发表时间：
2020-08-04
影响因子：
11.1
通讯作者：
Finkelstein, Ilya J.
中科院分区：
文献类型：
--
作者：
Press, William H.;Hawkins, John A.;Finkelstein, Ilya J.
合成DNA正在迅速崛起，成为一种持久的、高密度的信息存储平台。基于DNA的信息编码策略的一个主要挑战是在DNA合成和测序过程中出现的高错误率。这里，我们描述了修复所有三种基本类型的DNA错误的纠错码(Hash编码，贪婪穷举搜索解码)：插入、删除和替换。对冲还将未解决的或复合的错误转换为替换，通过跨链交织的标准里德-所罗门外码恢复同步以进行纠正。此外，对冲可以包含一大类用户定义的序列限制，例如避免过多重复，或过高或过低的窗口型鸟嘌呤胞嘧啶(GC)含量。我们通过电子计算机模拟和合成DNA来测试我们的代码。根据其测量的性能，我们开发了一个适用于更大数据集的统计模型。预测的性能表明，从退化的DNA中无错误恢复PB级和EB级数据的可能性高达10%。随着DNA合成和测序成本的持续下降，我们预计模糊限制语将在大规模无错误信息编码中得到应用。
Synthetic DNA is rapidly emerging as a durable, high-density information storage platform. A major challenge for DNA-based information encoding strategies is the high rate of errors that arise during DNA synthesis and sequencing. Here, we describe the HEDGES (Hash Encoded, Decoded by Greedy Exhaustive Search) error-correcting code that repairs all three basic types of DNA errors: insertions, deletions, and substitutions. HEDGES also converts unresolved or compound errors into substitutions, restoring synchronization for correction via a standard Reed-Solomon outer code that is interleaved across strands. Moreover, HEDGES can incorporate a broad class of user-defined sequence constraints, such as avoiding excess repeats, or too high or too low windowed guanine-cytosine (GC) content. We test our code both via in silico simulations and with synthesized DNA. From its measured performance, we develop a statistical model applicable to much larger datasets. Predicted performance indicates the possibility of error-free recovery of petabyte- and exabyte-scale data from DNA degraded with as much as 10% errors. As the cost of DNA synthesis and sequencing continues to drop, we anticipate that HEDGES will find applications in large-scale error-free information encoding.