Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
BACKGROUND
- Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients.


OBJECTIVE
- To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided.


METHODS
- Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance.


CONCLUSIONS
- Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.
From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock).
Robert
R
Schlaberg
From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock).
Charles Y
CY
Chiu
From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock).
Steve
S
Miller
From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock).
Gary W
GW
Procop
From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock).
George
G
Weinstock
From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock).
From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock).
D000465:Algorithms; D064790:Clinical Laboratory Services / Q000592:standards*; D003141:Communicable Diseases / Q000175:diagnosis / Q000382:microbiology*; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D056186:Metagenomics; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D013048:Specimen Handling; D057188:Workflow