UltraSEQ, a Universal Bioinformatic Platform for Information-Based Clinical Metagenomics and Beyond

Gemler, Bryan T; Mukherjee, Chiranjit; Howland, Carrie A.; Fullerton, Patrick A; Spurbeck, Rachel R.; Catlin, Lindsay A.; Smith, Anthony K.; Minard-Smith, Angela; Bartling, Craig M.

doi:10.1128/spectrum.04160-22

Cited by 4 publications

(1 citation statement)

References 37 publications

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“…Gemler et al (2023) introduced the UltraSEQ pipeline and compared its performance to several commercially available options. They evaluated these pipelines using publicly available clinical datasets from various samples and data formats, including short- and long-reads [ 111 ]. This study exemplifies the efforts underway to refine and improve bioinformatic tools for metagenomics.…”

Section: Need For Identification Of the Best-use Practices That Accel...mentioning

confidence: 99%

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Spatz,

Afonso

2024

Veterinary Sciences

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Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology’s operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the “core” of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through “implementation research” by a consortium of interested institutions working on common samples.

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Section: Need For Identification Of the Best-use Practices That Accel...mentioning

confidence: 99%