Comparing Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes
Author Information
Author(s): Sam Lee T., Doron Lipson, Tal Raz, Xuhong Cao, John Thompson, Patrice M. Milos, Dan Robinson, Arul M. Chinnaiyan, Chandan Kumar-Sinha, Christopher A. Maher
Primary Institution: University of Michigan
Hypothesis
What are the differences in transcript coverage and detection sensitivity between single-molecule sequencing and amplification-based sequencing in cancer transcriptomes?
Conclusion
Single-molecule sequencing provides better coverage of low-abundance transcripts compared to amplification-based sequencing, which tends to over-represent high-abundance transcripts.
Supporting Evidence
- Single-molecule sequencing was able to sequence lower-abundance transcripts more thoroughly than amplification-based sequencing.
- Amplification-based sequencing showed a characteristic coverage bias towards high abundance transcripts.
- SMS produced more alignable reads in absolute terms in 10 out of the 12 samples evaluated.
Takeaway
This study shows that one way of reading DNA can find more hidden messages than another way, especially when the messages are quiet.
Methodology
The study compared RNA-Seq results from single-molecule sequencing and amplification-based sequencing across 12 cancer cell lines and tissue samples.
Potential Biases
Amplification-based sequencing may introduce biases by over-representing high-abundance transcripts.
Limitations
The study did not explore the effects of different aligners on the observed biases in transcript coverage.
Participant Demographics
The study involved human cancer cell lines and tissues, specifically prostate cancer samples.
Digital Object Identifier (DOI)
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