A comparison of single molecule and amplification based sequencing of cancer transcriptomes.
A comparison of single molecule and amplification based sequencing of cancer transcriptomes.
复制标题
DOI：
10.1371/journal.pone.0017305
复制
发表时间：
2011-03-01
期刊：
影响因子：
3.7
通讯作者：
Maher CA
中科院分区：
文献类型：
--
作者：
Sam LT;Lipson D;Raz T;Cao X;Thompson J;Milos PM;Robinson D;Chinnaiyan AM;Kumar-Sinha C;Maher CA
The second wave of next generation sequencing technologies, referred to as single-molecule sequencing (SMS), carries the promise of profiling samples directly without employing polymerase chain reaction steps used by amplification-based sequencing (AS) methods. To examine the merits of both technologies, we examine mRNA sequencing results from single-molecule and amplification-based sequencing in a set of human cancer cell lines and tissues. We observe a characteristic coverage bias towards high abundance transcripts in amplification-based sequencing. A larger fraction of AS reads cover highly expressed genes, such as those associated with translational processes and housekeeping genes, resulting in relatively lower coverage of genes at low and mid-level abundance. In contrast, the coverage of high abundance transcripts plateaus off using SMS. Consequently, SMS is able to sequence lower- abundance transcripts more thoroughly, including some that are undetected by AS methods; however, these include many more mapping artifacts. A better understanding of the technical and analytical factors introducing platform specific biases in high throughput transcriptome sequencing applications will be critical in cross platform meta-analytic studies.
登录
查看更多内容
影响因子：
14.9
作者：
Bruford, Elspeth A.;Lush, Michael J.;Wright, Mathew W.;Sneddon, Tam P.;Povey, Sue;Birney, Ewan
通讯作者：
Birney, Ewan
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
158.5
作者：
Shah, Sohrab P.;Koebel, Martin;Huntsman, David G.
通讯作者：
Huntsman, David G.
影响因子：
30.8
作者：
Campbell, Peter J.;Stephens, Philip J.;Pleasance, Erin D.;O'Meara, Sarah;Li, Heng;Santarius, Thomas;Stebbings, Lucy A.;Leroy, Catherine;Edkins, Sarah;Hardy, Claire;Teague, Jon W.;Menzies, Andrew;Goodhead, Ian;Turner, Daniel J.;Clee, Christopher M.;Quail, Michael A.;Cox, Antony;Brown, Clive;Durbin, Richard;Hurles, Matthew E.;Edwards, Paul A. W.;Bignell, Graham R.;Stratton, Michael R.;Futreal, P. Andrew
通讯作者：
Futreal, P. Andrew
影响因子：
56.9
作者：
Tomlins, SA;Rhodes, DR;Chinnaiyan, AM
通讯作者：
Chinnaiyan, AM