Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics

Abstract

Thanks to personalized medicine trends and collaborations between industry, clinical research groups and regulatory agencies, next generation sequencing (NGS) is turning into a common practice faster than one could have originally expected. When considering clinical applications of NGS in oncology, a rapid workflow for DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples, as well as producing high quality library preparation, can be real challenges. Here we consider these targets and how applying effective automation technology to NGS workflows may help improve yield, timing and quality-control. We firstly evaluated DNA recovery from archived FFPE blocks from three different manual extraction methods and two automated extraction workstations. The workflow was then implemented to somatic (lung/colon panel) and germline (BRCA1/2) library preparation for NGS analysis exploiting two automated workstations. All commercial kits gave good results in terms of DNA yield and quality. On the other hand, the automated workstation workflow has been proven to be a valid automatic extraction system to obtain high quality DNA suitable for NGS analysis (lung/colon Ampli-seq panel). Moreover, it can be efficiently integrated with an open liquid handling platform to provide high-quality libraries from germline DNA with more reproducibility and high coverage for targeted sequences in less time (BRCA1/2). The introduction of automation in routine workflow leads to an improvement of NGS standardization and increased scale up of sample preparations, reducing labor and timing, with optimization of reagents and management.

Implementation of preventive and predictive BRCA testing in patients with breast, ovarian, pancreatic, and prostate cancer: a position paper of Italian Scientific Societies

“…Moreover, at the analytical level, the type of laboratory layout can still influence the quality and the tourn around time of assays, particularly when the automated and manual processes are compared. 39 However, the coverage and the filtering criteria of variant can also affect the quality of variant reporting. 40 …”

Cutting-edge technology and automation in the pathology laboratory

“…New technologies, including digital pathology systems and artificial intelligence techniques, are being developed and applied to enhance diagnostic accuracy, though adoption has been gradual due to concerns about data privacy, cost, and compatibility [ 6 , 7 ]. Also, molecular pathology provides results that need to be precise and require standardized analytical procedures before implementation [ 8 ]. In this setting, quality assurance and control systems play a crucial role, serving as adjuvants to ensure the accuracy and reliability of results [ 9 – 11 ].…”

Automation of hybridization and capture based next generation sequencing library preparation requires reduction of on-deck bead binding and heated wash temperatures

“…Muscarella et al used open-platform liquid handling to automate NGS library preparation for a breast cancer panel and found that automation decreased their processing time from two working days to one without substantially changing library quality [7] . Klevebring et al observed a significant improvement in quality consistency among cDNA libraries generated on a robotic workstation [8] .…”