Mar 29, 2020

Internal Control for process monitoring of clinical metagenomic next-generation sequencing of urine samples

BioRxiv : the Preprint Server for Biology
Victoria A. JanesC. Schultsz

Abstract

Background: Process control for clinical metagenomic next-generation sequencing (mNGS) is not yet widely applied, while technical sources of bias are plentiful. We present an easy-to-use internal control (IC) method focussing on technical process control applied to metagenomics in clinical diagnostics. Methods: DNA of nine urine samples was sequenced in the absence and presence of Thermus thermophilus DNA as IC in incremental concentrations (0.5-2-5%). Between aliquots of each sample, we compared the IC relative abundance (RA), and after in silico subtraction of IC reads, the microbiota and the RA of pathogens. The optimal IC spike-in concentration was defined as the lowest concentration still detectable in all samples. Results: The RA of IC correlated linearly with the spiked IC concentration (r2=0.99). IC added in a concentration of 0.5% of total DNA concentration was detectable in all samples, regardless of human/bacterial composition and after in silico removal gave the smallest difference in RA of pathogens compared to the unspiked aliquot of the sample. The microbiota of sample aliquots sequenced in the presence and absence of IC was highly similar (median BC-dissimilarity per sample of 0.059), provided samples had suffic...Continue Reading

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