Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments.
Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments.
复制标题
DOI：
10.1186/1471-2105-13-s6-s4
复制
发表时间：
2012-04-19
影响因子：
3
通讯作者：
Gelfand MS
中科院分区：
文献类型：
--
作者：
Khrameeva EE;Gelfand MS
整个基因组和转录本的高通量测序使人们能够非常快速地以低成本产生大量序列数据。大多数mRNA测序研究的目的是比较不同样本之间的表达水平。然而，考虑到现代测序方案、平台及其版本的广泛多样性，尚不清楚所获得的结果在多大程度上在不同平台和实验室之间是一致的。在Illumina和Solid平台上对全球26个机构进行的117项人类mRNA和基因组高通量测序实验的比较表明，基因覆盖率对生产实验室的依赖程度很高。基因覆盖图谱显示，实验室特有的非一致性经受住了3‘-偏见校正和可映射性标准化，这表明还有其他未知的与mRNA相关的偏见。
High-throughput sequencing of whole genomes and transcriptomes allows one to generate large amounts of sequence data very rapidly and at a low cost. The goal of most mRNA sequencing studies is to perform the comparison of the expression level between different samples. However, given a broad variety of modern sequencing protocols, platforms and versions thereof, it is not clear to what extent the obtained results are consistent across platforms and laboratories. The comparison of 117 human mRNA and genome high-throughput sequencing experiments performed on the Illumina and SOLiD platforms at 26 institutions all over the world demonstrated high dependency of the gene coverage profiles on the producing laboratory. Gene coverage profiles showed laboratory-specific non-uniformity that survived the 3'-bias correction and mappability normalization, suggesting that there are other yet unknown mRNA-associated biases.