A comparison of single molecule and amplification based sequencing of cancer transcriptomes

35Citations
Citations of this article
128Readers
Mendeley users who have this article in their library.

Abstract

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.

Cite

CITATION STYLE

APA

Sam, L. T., Lipson, D., Raz, T., Cao, X., Thompson, J., Milos, P. M., … Maher, C. A. (2011). A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS ONE, 6(3). https://doi.org/10.1371/journal.pone.0017305

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free