(1121-B) High-throughput preparation of NGS libraries for target-enriched DNA sequencing (whole exome sequencing) on the Biomek i7 Hybrid Workstation

Abstract: High-throughput preparation of NGS libraries for target-enriched DNA sequencing (whole
exome sequencing) on the Biomek i7 Hybrid Workstation

Elisa Vega
Senior Automation Scientist NGS
Roche Diagnostics, Wilmington, MA 01887, USA

Co-Authors: Sean Chien 2 , Zach Smith 3 , Jonathan Nowacki*, Alejandro Quiroz Zarate 1 , Marsha
McMakin 1 , Rachel Kasinskas 1
1 Roche Diagnostics, 200 Ballardvale St #250, Wilmington, MA 01887, USA
2 Roche Molecular Solutions, 4300 Hacienda Dr, Pleasanton, CA 94588, USA
3 Beckman Coulter Life Sciences ., 5350 Lakeview Parkway S. Dr., Indianapolis, IN 46268, USA
*Author no longer employee at Roche

Introduction
Whole-genome sequencing (WGS) with next-generation sequencing (NGS) technology has
driven a wide diversity of investigations and applications in human health. However, WGS
remains a high-cost method and often does not provide either the precision or depth of
information required to investigate complex diseases, or to detect rare or low-frequency
genetic variants. Enrichment of specific genomic regions through NGS target enrichment offers
a more economic path to deeper, more precise sequencing by focusing sequencing reads on
only the desired regions. Thus, target enrichment (such as whole-exome sequencing, or WES)
allows for more efficient use of sequencing resources, reduces sequencing cost, and simplifies
data analysis. Additional savings in cost, time, and labor – as well as increased throughput and
reproducibility – can be achieved through the automation of NGS library preparation and
through target enrichment on automated liquid handling instruments. Numerous standardized
NGS liquid handling platforms can expedite NGS workflows by offering out-of-the box solutions
for many popular reagent kits.

Methods
Automated preparation of WES libraries from hgDNA was carried out on the Biomek i7 Hybrid
Workstation using the KAPA HyperPlus Kit and KAPA HyperExome Panel, following the KAPA
HyperCap Workflow. Library preparation steps were processed in a high-throughput (96
samples) format, and then, for target capture, libraries were multiplexed in 12 pools of 8
libraries each (8-plex). All libraries were assessed for yield and fragment distribution before and
after target enrichment.

Results*
Pre-sequencing metrics demonstrated consistent yields and expected fragment distributions for
high-throughput processing, with minimal variation. Sequencing metrics revealed successful
enrichment of high-quality sequencing libraries with low duplication rates, high on-target rates,
and sufficient, uniform depth of coverage across the target regions.

Conclusion
Automation of the KAPA HyperCap workflow on the Biomek i7 Hybrid Workstation generated
high-quality WES libraries which, upon sequencing, yielded low duplication rates, high on-target
rates, and sufficient, uniform depth of coverage across the target regions.

*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.