A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library

Virology Journal

Johnson Mak³  Miles Davenport¹  Simon Mallal²  Abha Chopra²  Andrew Grimm¹  Deborah Cromer¹  Caryll Waugh³ 

[1]Centre for Vascular Research, University of NSW, Sydney, NSW, Australia

[2]Institute for Immunology and infectious diseases (IIID), Murdoch University, Perth, WA, Australia

[3]Biosecurity Flagship, CSIRO(AAHL), Geelong, VIC, Australia

关键词: Transfection;    Mutation rate;    Recombination rate;    HIV;   

Others  :  1225286
DOI  :  10.1186/s12985-015-0280-x

 received in 2014-12-03, accepted in 2015-03-16,  发布年份 2015

【 摘 要 】

Background

Massive, parallel sequencing is a potent tool for dissecting the regulation of biological processes by revealing the dynamics of the cellular RNA profile under different conditions. Similarly, massive, parallel sequencing can be used to reveal the complexity of viral quasispecies that are often found in the RNA virus infected host. However, the production of cDNA libraries for next-generation sequencing (NGS) necessitates the reverse transcription of RNA into cDNA and the amplification of the cDNA template using PCR, which may introduce artefact in the form of phantom nucleic acids species that can bias the composition and interpretation of original RNA profiles.

Method

Using HIV as a model we have characterised the major sources of error during the conversion of viral RNA to cDNA, namely excess RNA template and the RNaseH activity of the polymerase enzyme, reverse transcriptase. In addition we have analysed the effect of PCR cycle on detection of recombinants and assessed the contribution of transfection of highly similar plasmid DNA to the formation of recombinant species during the production of our control viruses.

Results

We have identified RNA template concentrations, RNaseH activity of reverse transcriptase, and PCR conditions as key parameters that must be carefully optimised to minimise chimeric artefacts.

Conclusions

Using our optimised RT-PCR conditions, in combination with our modified PCR amplification procedure, we have developed a reliable technique for accurate determination of RNA species using NGS technology.

【 授权许可】

   
2015 Waugh et al.; licensee BioMed Central.

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