(1114-C) Automated RNA-seq library preparation on the Beckman Coulter Biomek i7 Hybrid Automated Workstation using a shortened KAPA RNA HyperPrep workflow

Abstract: Automated RNA-seq library preparation on the Beckman Coulter Biomek i7 Hybrid Automated Workstation using a shortened KAPA RNA HyperPrep workflow

Amy Janiak
Senior Automation Support Scientist
Roche Diagnostics, Wilmington, MA 01887, USA

Co-Authors: Amy Janiak 1 , Amy Elias 1 , Elisa Vega 1 , Zach Smith 2 , Nikita Dsouza 1 , Alejandro Quiroz Zarate 1 ,
Marsha McMakin 1 , Rachel Kasinskas 1
1 Roche Diagnostics, 200 Ballardvale St #250, Wilmington, MA 01887, USA
2 Beckman Coulter Inc., 5350 Lakeview Parkway S. Dr., Indianapolis, IN 46268, USA

Introduction
As RNA sequencing (RNA-seq) has become more important to our understanding of disease and
to the development of new pharmaceuticals, the need for faster, scalable, reproducible
workflows has also grown. However, RNA-seq library preparation methods are complex and
require high levels of precision, posing a challenge to the required scaling and reproducibility. In
this study, a two-fold approach was taken to overcome these challenges: (1) a new, shorter
RNA-seq library prep workflow was developed using on-market kits without the need for
additional reagents, and (2) this shorter workflow was automated on a liquid handler that is
frequently used for NGS library preparation.

Methods
A new, shorter workflow for the KAPA RNA HyperPrep Kit with RiboErase (HMR) was automated
on the Beckman Coulter Biomek i7 Hybrid Automated Workstation. High-quality UHR RNA was
used as input across a 40-fold range of input amounts (25 ng, 250 ng, and 1000 ng). For
comparison, RNA-seq libraries were also prepared manually using the standard workflow.

Results*
The total library yield and size distribution of libraries prepared on the Biomek i7 Workstation
using the shorter workflow were comparable to manually prepared libraries. More
importantly, RNA-seq QC metrics — such as duplication rate, rRNA removal, and number of
reads mapped to the genome — were comparable between the two methods.

Conclusions
These metrics demonstrate that this fast, shorter, automated method increases speed and
reproducibility of RNA–seq library prep without impacting accuracy or efficiency of the KAPA
RNA HyperPrep Kit. Thus, together, these new workflows reduce the amount of hands-on time
required, improve reproducibility, and enable higher sample throughput for RNA library
preparation.

*Data on file at Roche Diagnostics, Wilmington, MA, USA

For Research Use Only. Not for use in diagnostics procedures. KAPA is a trademark of Roche.
Biomek is a trademark of Beckman Coulter Life Sciences.