Standardization and quality management in next-generation sequencing

Christoph Endrullat, Jörn Glökler, Philipp Franke, Marcus Frohme, Christoph Endrullat, Jörn Glökler, Philipp Franke, Marcus Frohme

Abstract

DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.

Keywords: ABRF, Association of Biomolecular Resource Facilities; BAM, binary alignment/map; CAP, College of American Pathologist's; CEN, European Committee for Standardization; CLIA, Clinical Laboratory Improvement Amendments; Data quality; ERCC, External RNA Controls Consortium; FDA, Food and Drug Administration; FFPE, formalin-fixed, paraffin-embedded; FMEA, failure mode and effects analysis; GATK, genome analysis toolkit; GSC, Genomic Standards Consortium; Guideline; HGP, Human Genome Project; Indel, insertion or deletion; MAQC, MicroArray Quality Control Project; MIGS, minimum information about a genome sequence; MOL, molecular pathology checklist; NGS, next-generation sequencing; NIST, National Institute of Standards and Technology; NTC, no-template control; Nex-StoCT, next generation sequencing — standardization of clinical testing; Next-generation sequencing; PT, proficiency testing; QA, quality assurance; QC, quality control; QM, quality management; QMS, quality management system; Quality management; RIN, RNA integrity number; SAM, sequence alignment/map; SEQC, sequencing quality control; SNP, single nucleotide polymorphism; SOP, standard operating procedure; Standardization; TN, technical note; VCF, variant call format; Validation; ddPCR, digital droplet PCR; mtDNA, mitochondrial DNA; qPCR, quantitative PCR.

Figures

Fig. 1
Fig. 1
Overview of the general NGS workflow. The main steps library and template preparation, enrichment, sequencing and data analysis are divided into substeps containing recommendations for checkpoints which are proposed for QC.

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