title: A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library.
abstract: 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.
  
  
  METHODS
  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.
authors: School of Medicine, Deakin University and CSIRO(AAHL), Geelong, VIC, Australia. caryll.waugh@csiro.au.|Biosecurity Flagship, CSIRO(AAHL), Geelong, VIC, Australia. caryll.waugh@csiro.au.
authors: Caryll
authors: C
authors: Waugh
authors: Centre for Vascular Research, University of NSW, Sydney, NSW, Australia. d.cromer@unsw.edu.au.
authors: Deborah
authors: D
authors: Cromer
authors: Centre for Vascular Research, University of NSW, Sydney, NSW, Australia. a.grimm@unsw.edu.au.
authors: Andrew
authors: A
authors: Grimm
authors: Institute for Immunology and infectious diseases (IIID), Murdoch University, Perth, WA, Australia. a.chopra@iiid.com.au.
authors: Abha
authors: A
authors: Chopra
authors: Institute for Immunology and infectious diseases (IIID), Murdoch University, Perth, WA, Australia. S.Mallal@murdoch.edu.au.
authors: Simon
authors: S
authors: Mallal
authors: Centre for Vascular Research, University of NSW, Sydney, NSW, Australia. M.Davenport@unsw.edu.au.
authors: Miles
authors: M
authors: Davenport
authors: School of Medicine, Deakin University and CSIRO(AAHL), Geelong, VIC, Australia. j.mak@deakin.edu.au.|Biosecurity Flagship, CSIRO(AAHL), Geelong, VIC, Australia. j.mak@deakin.edu.au.
authors: Johnson
authors: J
authors: Mak
mesh_terms: D016477:Artifacts; D002460:Cell Line; D015723:Gene Library; D015658:HIV Infections / Q000175:diagnosis / Q000821:virology; D015497:HIV-1 / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods / Q000592:standards; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods / Q000592:standards; D016865:Reassortant Viruses / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods / Q000592:standards; D014162:Transfection / Q000379:methods / Q000592:standards