Aug 2026· Laboratoriums Medizin· Vol 57 5· 0 citations
Medicine
TL;DR
This work sought to systematically apply CAP laboratory-developed test validation requirements for next-generating sequencing to targeted CFTR gene sequencing on an Illumina iSeq100 Sequencing System and to address assay-specific translational guidance gaps.
Tumor next-generation sequencing (NGS) is widely used to refine diagnosis and identify therapy targets. However, reporting criteria, schemas, and formats vary greatly which can affect uniformity of clinical cancer care. With the aim of promoting harmonization, the current state of NGS reporting practices was profiled across Genomics Organization for Academic Laboratories (GOAL) members. The assessment included a group landscape analysis to refine topics followed by a survey of member laboratories and post-survey discussions. A total of 28 surveys covering hematology and/or solid tumor panels from 21 academic laboratories were analyzed. A majority of responses indicated use of one or more variant tiering systems and reporting of all presumed somatic variants of uncertain significance. Most indicated significant manual effort by directors in generating final reports related to variant annotation using multiple external and internal laboratory databases, evaluation for potential germline variants, and correlation with prior NGS studies and clinical context. Report differences by indication related to more frequent inclusion of longitudinal comparisons for hematologic neoplasms and potential therapies for solid tumor reports. Based on areas of strong consensus among survey participants, considerations for best practices are presented along with opportunities for future harmonization, which may require improvements in classification schemas or better software tools.
Celeste C. Eno, R. Sompallae, Daniel Jones et al.· Journal of Molecular Diagnos...· 0 citations
This mini-review synthesizes validation and regulatory challenges unique to mNGS-based diagnostics and describes how laboratories and developers currently navigate available pathways, focusing on core analytical and clinical validation challenges.
Nick P. G. Gauthier, Vishal Kapoor, David C. Gaston et al.· Journal of Clinical Microbio...· 0 citations
BACKGROUND
Metagenomic next-generation sequencing (mNGS) enables broad, untargeted detection of pathogens and microbial signals across complex sample types. However, the diversity of operational contexts, from regulatory enforcement to exploratory discovery, challenges the defining of analytical or interpretive standards appropriate across all applications. Variability in laboratory practices, bioinformatic methods, and reporting conventions continues to limit consistency and decision-maker confidence in mNGS results.
OBJECTIVES
We introduce STRATUM (Structured Framework for Reporting, Assessment, and Translational Utility of Metagenomics), a use-case-stratified framework that aligns quality assurance, metadata reporting, and interpretive standards with the consequence and intended use of metagenomic sequencing outputs.
METHODS
STRATUM is organized around five representative biosurveillance use cases spanning public health, food safety, environmental monitoring, synthetic biology detection, and national security. A three-tier interpretive model calibrates analytical rigor, validation expectations, and reporting requirements to decision consequence; from high-consequence regulatory and clinical determinations (Tier 1), through operational surveillance (Tier 2), to exploratory and hypothesis-generating contexts (Tier 3).
RESULTS
The framework provides graduated guidance across key domains including sample preparation, sequencing design, controls and contamination governance, reference database curation, bioinformatics reproducibility, and multi-factor signal validation. Cross-cutting principles include explicit documentation of evidentiary bases, transparency in database and pipeline provenance, and defined escalation pathways when results transition between interpretive tiers.
CONCLUSION
Realizing the operational potential of mNGS requires evidentiary standards responsive to decision context rather than fixed across applications. STRATUM offers a consequence-tiered model for quality and reporting in applied metagenomics, supporting reproducible, transparent, and defensible sequencing-based surveillance across public health and biodefense domains.
Unknown authors· Journal of AOAC Internationa...· 0 citations
Cell-free total nucleic acid (cfTNA)-based liquid biopsy (LBx) offers a minimally invasive alternative to tissue-based next generation sequencing (NGS). Most NGS-based LBx assays require several days for results. This study validated a rapid NGS-based LBx assay with a two-day turnaround time (TAT). Patient plasma samples were used to validate the Oncomine Precision Assay for single nucleotide variants (SNVs), insertion deletions (indels) and fusions across 50 genes on the Genexus Sequencer. Manual extraction using the QIAamp cfTNA Kit was performed to optimize fusion detection. Analytical sensitivity in synthetic controls (N=20) using the automated workflow was 99.2% for SNVs and 95% for indels, with 100% specificity (allele frequency ≥0.5%). In clinical samples (N=107), sensitivity was 99.4% for SNVs and 100% for indels; specificity was 100% for both, compared with orthogonal assays. Manual extraction improved overall performance compared to the automated extraction and was used for the final clinical workflow. Analytical sensitivity of fusions in synthetic controls (N=22) was 98.9%, with 100% specificity (≥7 copies). In clinical samples (N=38) sensitivity and specificity for both SNVs and indels were 100% and 99.9%, respectively; sensitivity for fusions was 72.2%; specificity was 100%. Overall precision was >99% and average TAT was ≤2 days. This study reports the feasibility and validation of a two-day TAT NGS-based cfTNA assay that can potentially reduce time-to-treatment.
S. Roy-Chowdhuri, Ana Galán-Cobo, N. Agarwal et al.· Journal of Molecular Diagnos...· 0 citations
ABSTRACT Whenever next generation sequencing is used in clinical and public health laboratories, rigorous quality control and quality assurance are key components of a quality management system. However, both the development and maintenance of a quality management system encompassing next generation sequencing present significant challenges, such as selection of appropriate sequencing platforms, complex workflows, allocation of time and resources, kit and reagent management, potential discontinuation of technical support, specialized bioinformatic workflows, compliance with regulatory and/or accreditation bodies, and the necessity of highly trained personnel. In an effort to address such challenges, the Centers for Disease Control and Prevention collaborated with public health partners to establish the Next Generation Sequencing Quality Initiative, which focuses on the development of a sequencing-focused quality management system. Here, we describe the ongoing efforts of the Next Generation Sequencing Quality Initiative to develop a foundational quality management system specific to next generation sequencing, as well as collaborations aimed to assist partners in addressing ongoing and emerging quality-related challenges associated with assay implementation in laboratories for surveillance and diagnostic applications.
Blake Cherney, Ariel Díaz, Christopher Ghattas et al.· Journal of Clinical Microbio...· 0 citations
Some of the recent work on dPCR-based RMPs are described and how this can be applied to improve nucleic acid analysis measurements on a global scale in EQA schemes, clinical laboratories and harmonization studies for infectious disease diagnostics are discussed.
S. Falak, D. O'Sullivan, Megan H. Cleveland et al.· 150th anniversary of the Met...· 0 citations
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