Next-generation Sequencing (NGS) Library Preparation on RACs

Authors: Paulina Kanigowska, Ph.D., Elizabeth Gendreau, Teryn Citino, Alicia Byrn, Brintha Girinathan, Aimable Habimana, Anna Peters, Noah Nsangou, Alycia Wong

Introduction

High-throughput genetic engineering necessitates frequent cost- and time-efficient iteration through the Design, Build, Test and Learn (DBTL) cycles. In recent years, next-generation sequencing (NGS) has significantly improved this iteration, becoming the go-to Test approach for verifying both successful DNA assembly of plasmids and genome engineering of microbial strains, at both academic and industrial biotech facilities2,3.

Here, we show how we successfully miniaturized (100-fold) and adapted the Illumina DNA Prep workflow to be end-to-end executed on Ginkgo’s RAC platform, including upstream microbial cell lysis, thereby enabling quick, crude, and low-cost (~$3/sample) DNA sequence verification of 100s to 1000s purified and unpurified input samples daily, with minimal human intervention.

Previously published studies have been primarily focusing on automation-enabled miniaturization of a more automation-friendly, but less flexible (with respect to the input sample amount), NexteraR XT DNA Library Prep workflow2,3. The most recent studies attempted to miniaturize the Illumina DNA Prep workflow 10-fold, albeit manually1. Our work demonstrates how careful biological workflow adaptation towards a fully automated solution and a robust automation platform can improve upon these efforts.