Indel-correcting DNA barcodes for high-throughput sequencing.
Indel-correcting DNA barcodes for high-throughput sequencing.
复制标题
DOI：
10.1073/pnas.1802640115
复制
发表时间：
2018-07-03
影响因子：
11.1
通讯作者：
Press WH
中科院分区：
文献类型：
--
作者：
Hawkins JA;Jones SK Jr;Finkelstein IJ;Press WH
现代高通量生物测定通过用称为“条形码”的独特DNA序列标记每个成员来研究单个成员的合并群体。DNA条形码经常被DNA合成和测序错误破坏，导致大量数据丢失和不正确的数据解释。在这里，我们描述了一种纠错策略，以提高DNA条形码的效率和统计能力。我们的策略准确地处理了DNA条形码中的插入和缺失（indels），这是DNA合成和测序过程中遇到的最常见的错误类型，导致准确性，效率和信噪比的数量级增加。随附的软件包使这些条形码的部署对于更广泛的实验科学家社区来说非常简单。许多大规模、高通量实验使用DNA条形码（DNA文库前的短DNA序列）来鉴定汇集的生物分子群体中的个体。然而，DNA合成和测序错误混淆了观察到的条形码的正确解释，并可能导致显著的数据丢失或虚假结果。从计算机科学中借用的广泛使用的纠错码（例如，Hamming，Levenshtein编码）不能正确解释DNA条形码中的插入和缺失（插入缺失），即使缺失是最常见的合成错误类型。在这里，我们提出并实验验证填充/截断的右端编辑（自由）条形码，纠正取代，插入和删除错误，即使这些错误改变条形码长度。FREE条形码的设计考虑到实验因素，包括平衡的鸟嘌呤-胞嘧啶（GC）含量，最小的均聚物运行和减少的内部发夹倾向。我们生成并包括具有不同长度和纠错水平的条形码列表，这些条形码可能在不同的高通量应用中有用，包括>106个单纠错16聚体，其在解码准确性、条形码长度和文库大小之间取得平衡。此外，将两个或更多个FREE代码连接到单个条形码中可以组合地增加可用的条形码空间，生成具有>1015个纠错条形码的列表。所包含的用于创建条形码库和解码测序条形码的软件是高效的，并且被设计为对于普通生物学社区是用户友好的。
Modern high-throughput biological assays study pooled populations of individual members by labeling each member with a unique DNA sequence called a “barcode.” DNA barcodes are frequently corrupted by DNA synthesis and sequencing errors, leading to significant data loss and incorrect data interpretation. Here, we describe an error correction strategy to improve the efficiency and statistical power of DNA barcodes. Our strategy accurately handles insertions and deletions (indels) in DNA barcodes, the most common type of error encountered during DNA synthesis and sequencing, resulting in order-of-magnitude increases in accuracy, efficiency, and signal-to-noise ratio. The accompanying software package makes deployment of these barcodes straightforward for the broader experimental scientist community. Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate filled/truncated right end edit (FREE) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced guanine-cytosine (GC) content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error correction levels that may be useful in diverse high-throughput applications, including >106 single-error–correcting 16-mers that strike a balance between decoding accuracy, barcode length, and library size. Moreover, concatenating two or more FREE codes into a single barcode increases the available barcode space combinatorially, generating lists with >1015 error-correcting barcodes. The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.
登录
查看更多内容
影响因子：
3
作者：
Buschmann T;Bystrykh LV
通讯作者：
Bystrykh LV
影响因子：
46.9
作者：
Kitzman, Jacob O.
通讯作者：
Kitzman, Jacob O.
使用纳米液液滴对单个细胞的高度平行基因组表达分析。
影响因子：
64.5
作者：
Macosko EZ;Basu A;Satija R;Nemesh J;Shekhar K;Goldman M;Tirosh I;Bialas AR;Kamitaki N;Martersteck EM;Trombetta JJ;Weitz DA;Sanes JR;Shalek AK;Regev A;McCarroll SA
通讯作者：
McCarroll SA
影响因子：
14.9
作者：
Lee DF;Lu J;Chang S;Loparo JJ;Xie XS
通讯作者：
Xie XS
影响因子：
14.8
作者：
Zilionis, Rapolas;Nainys, Juozas;Mazutis, Linas
通讯作者：
Mazutis, Linas