Preventing Cross Contamination with
Automated Walk-Away Library Prep

Contamination-Free, Worry-Free, Walk-Away Library Prep Automation

Automation of library preparation increases throughput, reduces labor costs, and eliminates many of the sources of human error. As most next generation sequencing (NGS) library preparation protocols include one or more polymerase chain reaction (PCR) steps, an on-deck thermal cycler is needed to achieve true walk-away automation. However, on deck thermal cyclers (ODTC) have the potential for introducing contamination. The Sciclone® G3 NGSx iQ workstation is specifically designed for hands free, walk away, high-throughput NGS sample processing with modern features such as: high capacity tip storage, on-deck thermal accessories, and highly reproducible liquid transfer technology. When used with PerkinElmer’s disposable PCR plate lid, the Sciclone® G3 NGSx iQ workstation prevents sample contamination and delivers consistent results.

To Analyze for Cross Contamination:

  • 96 libraries were produced from 140 ng of Human NA12878 genomic DNA using the NEXTFLEX® Pre-plated Automated Rapid XP DNA-seq kit on a Sciclone® NGSx iQ workstation
  • 10 µl of a 25 pg/µl unique identifiable spike-in control was added to each sample prior to library preparation
  • 3 cycles of PCR were performed on the ODTC and then analyzed informatically to identify any potential cross contamination


In order to eliminate cross contamination, each barcoded library must have one and only one spike-in amplicon control associated with it. As you can see in Figure 1, each library has only one spike-in amplicon control associated with it, therefore, each library was determined to be 100% pure.

Figure 1: No cross contamination between libraries or wells occurred during library prep due to the unique identifiable pattern of spike-in controls.


No cross contamination across sample wells occurred during a 96-library experiment using PerkinElmer’s disposable PCR plate lids and the Sciclone® G3 NGSx iQ workstation. This modern marvel is an automation friendly solution for advanced liquid handling and constructing NGS libraries.

For research use only. Not for use in diagnostic procedures.