Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.
Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.
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DOI：
10.1038/nbt.2972
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发表时间：
2014-09
影响因子：
46.9
通讯作者：
Mason, Christopher E.
中科院分区：
文献类型：
--
作者：
Li, Sheng;Tighe, Scull W.;Nicolet, Charles M.;Grove, Deborah;Levy, Shawn;Farmerie, William;Viale, Agnes;Wright, Chris;Schweitzer, Peter A.;Gao, Yuan;Kim, Dewey;Boland, Joe;Hicks, Belynda;Kim, Ryan;Chhangawala, Sagar;Jafari, Nadereh;Raghavachari, Nalini;Gandara, Jorge;Garcia-Reyero, Natalia;Hendrickson, Cynthia;Roberson, David;Rosenfeldr, Jeffrey;Smith, Todd;Underwood, Jason G.;Wang, May;Zumbo, Paul;Baldwin, Don A.;Grills, George S.;Mason, Christopher E.
高通量RNA测序（RNA-seq）极大地扩展了新基因组学发现的潜力，但各种各样的平台、协议和性能也产生了对全面参考数据的需求。在这里，我们描述了生物分子资源设施协会下一代测序（ABRF-NGS）对RNA-seq的研究。我们使用参考RNA标准品在15个实验室地点测试了重复实验，以在5个测序平台（Illumina HiSeq、Life Technologies的PGM和Proton、Pacific Biosciences RS和Roche的454）上测试4种方案（polyA选择、核糖核酸耗尽、大小选择和降解）。结果显示，在深度计数平台上，表达测量具有高的平台内和平台间一致性，但所有平台之间剪接点和变体检测的效率和成本高度可变。这些数据还表明，核糖体RNA消耗既可以使降解的RNA样品的有效分析，并容易与polyA富集的馏分进行比较。该研究为跨平台的RNA-seq标准化、评价和改进提供了广泛的基础。
High-throughput RNA sequencing (RNA-seq) dramatically expands the potential for novel genomics discoveries, but the wide variety of platforms, protocols and performance has created the need for comprehensive reference data. Here we describe the Association of Biomolecular Resource Facilities next-generation sequencing (ABRF-NGS) study on RNA-seq. We tested replicate experiments across 15 laboratory sites using reference RNA standards to test four protocols (polyA-selected, ribo-depleted, size-selected and degraded) on five sequencing platforms (Illumina HiSeq, Life Technologies’ PGM and Proton, Pacific Biosciences RS and Roche’s 454). The results show high intra-platform and inter-platform concordance for expression measures across the deep-count platforms, but highly variable efficiency and cost for splice junction and variant detection between all platforms. These data also demonstrate that ribosomal RNA depletion can both enable effective analysis of degraded RNA samples and be readily compared to polyA-enriched fractions. This study provides a broad foundation for cross-platform standardization, evaluation and improvement of RNA-seq.
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DOI：
10.1093/bioinformatics/btr247
发表时间：
2011-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Łabaj PP;Leparc GG;Linggi BE;Markillie LM;Wiley HS;Kreil DP
通讯作者：
Kreil DP
来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
14.9
作者：
Hansen KD;Brenner SE;Dudoit S
通讯作者：
Dudoit S
影响因子：
48
作者：
Katz, Yarden;Wang, Eric T.;Airoldi, Edoardo M.;Burge, Christopher B.
通讯作者：
Burge, Christopher B.
影响因子：
46.9
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
通讯作者：
Pallen, Mark J.