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

1. PLoS One. 2011 Mar 1;6(3):e17305.

A comparison of single molecule and amplification based sequencing of cancer transcriptomes.
Sam LT, Lipson D, Raz T, Cao X, Thompson J, Milos PM, Robinson D, Chinnaiyan AM, 
Kumar-Sinha C, Maher CA.

Michigan Center for Translational Pathology, University of Michigan, Ann Arbor,
Michigan, United States of America.

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.


PMID: 21390249 [PubMed - in process]