Comparison of three targeted enrichment strategies on the SOLiD sequencing platform.
Comparison of three targeted enrichment strategies on the SOLiD sequencing platform.
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DOI：
10.1371/journal.pone.0018595
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发表时间：
2011-04-29
期刊：
影响因子：
3.7
通讯作者：
Gilbert JR
中科院分区：
文献类型：
--
作者：
Hedges DJ;Guettouche T;Yang S;Bademci G;Diaz A;Andersen A;Hulme WF;Linker S;Mehta A;Edwards YJ;Beecham GW;Martin ER;Pericak-Vance MA;Zuchner S;Vance JM;Gilbert JR
尽管下一代测序 (NGS) 的通量不断增加且成本稳步下降，但人类全基因组测序对于大多数遗传学实验室来说仍然不是一个可行的选择。在复杂疾病研究的情况下尤其如此，因为通常需要大量样本集才能获得足够的统计功效。为了充分利用 NGS 技术在大样本集上的潜力，已经开发了几种方法来选择性地富集感兴趣的区域。与全基因组测序相比，富集降低了金钱和计算成本，同时允许研究人员利用 NGS 通量。目前有几种靶向富集方法可用，包括分子倒置探针连接测序 (MIPS)、基于寡核苷酸杂交的方法和基于 PCR 的策略。为了评估这些方法与 ABI SOLID3+ 结合使用时的表现，我们研究了三种富集技术：基于 Nimblegen 寡核苷酸杂交阵列的捕获；基于 Agilent SureSelect 寡核苷酸杂交溶液的捕获；以及Raindance Technologies 的基于多重PCR 的方法。目标区域选自整个人类基因组的外显子和进化保守区域。使用各自的信息学流程对所有三种方法进行探针和引物对设计。总之，对于所有 3 种方法，大约 0.8 Mb 的目标空间是相同的。对 SOLiD 测序结果进行了多项指标分析，包括样本覆盖深度的一致性、目标与脱靶效率、等位基因偏差以及基因型与基于阵列的基因分型数据的一致性。 Agilent SureSelect 表现出卓越的目标效率和样品读取深度的相关性。 Nimblegen 在 20 倍及以下的读取深度下的性能相似。 Raindance 和 Nimblegen SeqCap 都在平均值附近表现出更紧密的读取深度分布，但在我们的实验中，两者的目标效率都较低。飞雨展示了检测设计中最高的多功能性。
Despite the ever-increasing throughput and steadily decreasing cost of next generation sequencing (NGS), whole genome sequencing of humans is still not a viable option for the majority of genetics laboratories. This is particularly true in the case of complex disease studies, where large sample sets are often required to achieve adequate statistical power. To fully leverage the potential of NGS technology on large sample sets, several methods have been developed to selectively enrich for regions of interest. Enrichment reduces both monetary and computational costs compared to whole genome sequencing, while allowing researchers to take advantage of NGS throughput. Several targeted enrichment approaches are currently available, including molecular inversion probe ligation sequencing (MIPS), oligonucleotide hybridization based approaches, and PCR-based strategies. To assess how these methods performed when used in conjunction with the ABI SOLID3+, we investigated three enrichment techniques: Nimblegen oligonucleotide hybridization array-based capture; Agilent SureSelect oligonucleotide hybridization solution-based capture; and Raindance Technologies' multiplexed PCR-based approach. Target regions were selected from exons and evolutionarily conserved areas throughout the human genome. Probe and primer pair design was carried out for all three methods using their respective informatics pipelines. In all, approximately 0.8 Mb of target space was identical for all 3 methods. SOLiD sequencing results were analyzed for several metrics, including consistency of coverage depth across samples, on-target versus off-target efficiency, allelic bias, and genotype concordance with array-based genotyping data. Agilent SureSelect exhibited superior on-target efficiency and correlation of read depths across samples. Nimblegen performance was similar at read depths at 20× and below. Both Raindance and Nimblegen SeqCap exhibited tighter distributions of read depth around the mean, but both suffered from lower on-target efficiency in our experiments. Raindance demonstrated the highest versatility in assay design.
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影响因子：
46.9
作者：
Tewhey, Ryan;Warner, Jason B.;Nakano, Masakazu;Libby, Brian;Medkova, Martina;David, Patricia H.;Kotsopoulos, Steve K.;Samuels, Michael L.;Hutchison, J. Brian;Larson, Jonathan W.;Topol, Eric J.;Weiner, Michael P.;Harismendy, Olivier;Olson, Jeff;Link, Darren R.;Frazer, Kelly A.
通讯作者：
Frazer, Kelly A.
影响因子：
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作者：
PARZEN, E
通讯作者：
PARZEN, E
影响因子：
3.9
作者：
Melum, Espen;May, Sandra;Franke, Andre
通讯作者：
Franke, Andre
影响因子：
46.9
作者：
Gnirke A;Melnikov A;Maguire J;Rogov P;LeProust EM;Brockman W;Fennell T;Giannoukos G;Fisher S;Russ C;Gabriel S;Jaffe DB;Lander ES;Nusbaum C
通讯作者：
Nusbaum C
影响因子：
14.8
作者：
Hodges, Emily;Rooks, Michelle;Xuan, Zhenyu;Bhattacharjee, Arindam;Gordon, D. Benjamin;Brizuela, Leonardo;McCombie, W. Richard;Hannon, Gregory J.
通讯作者：
Hannon, Gregory J.