Standardization in next-generation sequencing - Issues and approaches of establishing standards in a highly dynamic environment

Abstract

Introduction 2nd generation sequencing or better known as next-generation sequencing (NGS) represents a cutting-edge technology in life sciences and current foundation for unravelling nucleotide sequences. Since advent of first platforms in 2005 the number of different types of NGS platforms increased in the last 10 years in the same manner as the variety of possible applications. Higher throughput, lower cost and better quality of data were the incentive for a range of enterprises developing new NGS devices, whereas economic issues and competitive pressure, based on expensive workflows of obsolete systems and decreasing cost of market leader platforms, resulted simultaneously in accelerated vanishing of several companies. Due to the fast development, NGS is currently characterized by a lack of standard operating procedures, quality management/quality assurance specifications, proficiency testing systems and even less approved standards along with high cost and uncertainty of data quality. On the one hand, appropriate standardization approaches were already performed by different initiatives and projects in the format of accreditation checklists, technical notes and guidelines for validation of NGS workflows. On the other hand, these approaches are exclusively located in the US due to origins of NGS overseas, therefore there exists an obvious lack of European-based standardization initiatives. An additional problem represents the validity of promising standards across different NGS applications. Due to highest demands and regulations in specific areas like clinical diagnostics, the same standards, which will be established there, will not be applicable or reasonable in other applications. These points emphasize the importance of standardization in NGS mainly addressing the laboratory workflows, which are the prerequisite and foundation for sufficient quality of downstream results. Methods This work was based on a platform-dependent and -independent systematic literature review as well as personal communications with i.a. Illumina, Inc., ISO/TC 276 as well as DIN NA 057-06-02 AA 'Biotechnology'. Results Prior formulation of specific standard proposals and collection of current de facto standards, the problems of standardization in NGS itself were identified and interpreted. Therefore, a variety of different standardization approaches and projects from organizations, societies and companies were reviewed. Conclusions There is already a distinct number of NGS standardization efforts present; however, the majority of approaches target the standardization of the bioinformatics processing pipeline in the context of “Big Data”. Therefore, an essential prerequisite is the simplification and standardization of wet laboratory workflows, because respective steps are directly affecting the final data quality and thus there exists the demand to formulate experimental procedures to ensure a sufficient final data output quality.

The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

“…This complex - and dynamic - reality poses a challenge for the implementation of bioinformatics pipelines in regulatory settings, where the demonstration of reliability and reproducibility is crucial (see also 11 , 29 ). Harmonisation approaches must face the variability described above in terms of technologies, strategies, and software used, each with their demonstrated success, limitations and caveats.…”