Whitepaper: Reducing Contamination, Complexity, and Cost in mNGS
High per-sample costs, reagent contamination, and multi-step workflows remain the three biggest barriers preventing metagenomic next-generation sequencing (mNGS) from reaching routine clinical use. This whitepaper presents the PaRTI-Seq workflow — an integrated approach that addresses all three challenges in a single, streamlined protocol.
Key Findings
- Host DNA interference is the primary cost driver in mNGS. Without pre-sequencing depletion, over 99% of reads map to the human genome, inflating sequencing depth requirements and downstream analysis time.
- The Devin host depletion filter removes approximately 99% of human nucleated cells in under five minutes, enabling pathogen identification with as few as 5 million reads — a four-fold reduction in sequencing depth compared to standard protocols.
- Reagent contamination introduces false-positive signals that vary by brand and lot, triggering costly retesting cycles. mNGS-grade reagents with lot-specific certificates of analysis eliminate this variable.
- Purpose-built bioinformatics filtering reduces raw organism calls from hundreds to confirmed pathogens by applying system control subtraction and fold-change thresholds.
The PaRTI-Seq Workflow
The whitepaper details a four-stage workflow designed to reduce per-sample cost while improving microbial read yield. Stage one uses the Devin filter for rapid, reagent-free host cell removal from liquid biopsies. Stage two employs the Devin Microbial Enrichment Kit with mNGS-grade reagents for contamination-controlled DNA extraction. Stage three constructs sequencing libraries using the Unison Ultralow DNA Library Prep Kit, optimized for the low DNA inputs typical of host-depleted samples. Stage four runs PaRTI-Seq Analysis — a curated bioinformatics platform covering over 1,400 pathogens — to deliver species-level identification with genome coverage verification.
Together, these stages produce 10 to 1,000 times more microbial reads than standard protocols, enabling laboratories to process four times more samples per sequencing run and reduce per-sample sequencing cost by up to 75%.
Download
Download the Full Whitepaper (PDF)
Products referenced in this whitepaper: – PaRTI-Seq Analysis – Devin Host Depletion Filter
