Improve the efficiency of the Sanger sequencing workflow with a new browser-based software platform for capillary electrophoresis (CE)

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In 1997, Sanger, Nicklen, and Coulson described a method for determining DNA nucleotide sequences.¹ Nearly five decades later, Sanger sequencing remains an entrenched technology for targeted sequencing and fragment analysis.

Accuracy and unambiguous results are the strengths of Sanger sequencing. Without dependence on algorithms, tuning and intensive data analysis, the peak is the peak and easy to compare with a reference. When focusing on a specific gene, mutation or sequence, the high specificity and sensitivity of Sanger sequencing prevails.

Sanger sequencing is widely used in infectious and rare disease research, vaccine development and mRNA QC, as well as in genome editing and plasmid confirmation. Unfortunately, many supporting software platforms have not kept pace with the growing needs of the biopharmaceutical, service provider and diagnostic markets
require process automation and secure data management in one
user-friendly format.

Enabling automation and compliance

Thermo Fisher Scientific’s new InnoviGene™ Suite is an all-in-one, browser-based platform that provides a suite of Sanger sequencing applications to enable regulatory compliance while increasing quality and productivity in a streamlined automated workflow.

“The user-friendly approach sets the InnoviGene Suite apart from many other bioinformatics suites that have more complicated menus and data management. The platform feels designed so that a new user can get started in under 10 minutes,” said Wesley Morovic, PhD, Senior Research Scientist at Thermo Fisher Scientific’s PPD™ clinical research division.

The same SAE (security, audit, e-signature) model is used on both the InnoviGene Suite and the Applied Biosystems SeqStudio Flex Genetic Analyzer to support full automation of data analysis functions for increased efficiency and shorter turnaround times. Additionally, the InnoviGene Suite optimizes the use of the Applied Biosystems BigDye Terminator Sequencing kit to improve data quality and reduce the need for resequencing.

There are currently two software modules available. The Sequence Quality Check module provides simple analysis, assessment and reporting of sequence data and quality metrics, with the added benefit of AI-based Smart Deep Basecaller for high-throughput scenarios. Compliance with 21 CFR Part 11 is achieved with a dedicated console that enables electronic records, user management, tracking and process monitoring.

The Sequence Identity module is designed for accurate sample sequence confirmation and identification of mismatches against a reference. This module helps mRNA QC manufacturers determine specimen characteristics and verify the accuracy of synthesized mRNA. This module is also particularly useful for plasmid sequencing.

InnoviGene in action

PPD’s clinical research business provides global services for contract research organizations (CRO) to deliver end-to-end, full-service solutions and customized strategies covering every aspect of clinical testing. Morovic provides analytical services for gene and cell therapies with a focus on DNA sequencing methods.

For the identification of drug components for gene and cell therapy, Thermo Fisher has a robust Sanger sequencing platform. The core of the process is trace quality control, sequence generation, quality trimming and assembly. Sanger sequencing applications range from transgene identification for recombinant AAVs, mRNA sequencing
identity for vaccines, to the identity of the plasmids used to produce
therapeutic substances.

PPD’s IT installation team must qualify any new software or equipment to ensure proper management according to company quality standards. A primary consideration is compliance with 21 CFR Part 11, including controls such as increased security measures, audit trails, and report generation.

After evaluating the InnoviGene Suite, Morovic highlighted that “InnoviGene has the potential to help reduce much of the complexity that historically still exists with many software platforms when performing quality assessment and data management of our Sanger sequencing measurements.”

Companies involved in next-generation drug development now have access to a new unified, browser-based CE software platform with enhanced built-in automated capabilities to manage Sanger sequencing assays and results.

Reference
1. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci US A. 1977 Dec; 74(12):5463-7. doi: 10.1073/pnas.74.12.5463.

More information thermofisher.com

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