Frequently Asked Questions
Devin can be used for all types of body fluids including whole blood, plasma, swabs, cerebrospinal fluid (CSF), bronchoalveolar lavage fluid (BALF), ascitic and other body fluids containing significant human DNA interference.
Devin™ filter exploits patented antifouling Zwitterionic coating technology (ZISC, Pic. 1) to specifically binds to human nucleated cells (>99%, Fig. 1), while allowing most of microorganisms (including bacteria, viruses, fungi etc.) to go through the filter intact (Fig. 2)
In comparison with other depletion methods (Fig. 3) Devin™ filter shows much faster processing time (less than 5 minutes) and greater portion of microbial sequencing reads. You can learn more about Devin™ filter, ZISC technology and its comparison with other depletion methods in White Paper: Needle in the Haystack: How to Remove Human Background When You Want to Detect Microorganisms
We recommend to use only fresh samples (immediately after blood or other body fluid was withdrawn from the patient with storage NOT exceeding 6 hours at ambient temperature or 12 hours at 2-6°C) for sample preparation with Devin™ filter. We have no data at the moment but strongly suspect that stored blood or frozen blood or extensive lysis probably will affect the efficacy of the filter, depending on the freezing and storage condition of the samples. If you have interest to test efficacy of Devin™ filter for frozen/stored clinical samples, we are delighted to invite you to collaborate with us and join Clinical Research Program
Theoretically Devin™ filter removes nucleated host (human) cells with intracellular viruses or bacteria which are unlikely to be recoverable from the filtrate obtained after fractionation. As the fractionation process is not pore-size based, fungal, yeasts, and protozoan cells will be enrichable and detectable (i.e. not retained by Devin™ filter). Analytical and clinical validation of the efficacy of detection of specific important targets is recommended.
*** If you have interest to test detection efficacy of Devin™ filter for intracellular viruses or bacteria using clinical samples, we are delighted to invite you to collaborate with us and join Clinical Research Program.
Recommended volume of specimen 2-10 ml. If volume is less than 2 ml, saline or a suitable mild buffer may be used to minimize dead volume loss.
PaRTI-Seq™ utilizes optimized workflow of sample preparation for next generation sequencing (NGS) and proprietary analytical methods, which provides precise test results within 24 hours upon sample receival.
You can learn more about PaRTI-Seq™ and how it works in the White Paper Optimizing sequencing costs in metagenomics. How to reduce costs of pathogen detection in with PaRTI-Seq™
PaRTI-Seq™ can be used for detection of various microorganisms like bacteria, fungi, viruses etc. You can learn more about clinical test results here.
Micronbrane’s database includes more than 1400 known human pathogens for immediate identification. Unknown novel exotic pathogens with no known sequences in Micronbrane’s database may also be uncovered through bioinformatic deep analysis of unaligned sequences against the full Genbank database.
*** Currently we have limited data on viruses, yeasts, filamentous fungi, parasites and intracellular bacteria. If you have interest to participate in testing these pathogens using clinical samples, we are delighted to invite you to collaborate with us and join “Clinical Research Program” to test more sample types (Check all areas of research interest here.
Human reads represent most of total sequencing reads (70% to 99%). Hence host DNA interference incurs the biggest portion of sequencing cost. A library prep workflow without host depletion, while theoretically possible, would be economically and practically unjustifiable. By removing most of host DNA interference PaRTI-Seq™ and Devin™ make possible to significantly optimize downstream sequencing cost and shorten sequencing time. Devin™ filter removes over 99% of nucleated cells from the sample and elevates the portion of microbial sequencing reads, reaching high sensitivity with less number of sequencing reads. Thus the typical output requirement of 20 mln sequencing reads for whole blood samples, for instance, can be reduced to up to 5 mln sequencing reads without loss of sensitivity. You can learn more how PaRTI-Seq™ helps to reduce up to 75% of sequencing cost in the White Paper Optimizing sequencing costs in metagenomics. How to reduce costs of pathogen detection in with PaRTI-Seq™
Currently our downstream NGS library kit is designed for DNA viruses. It does not have a reverse transcription step to detect and sequence RNA viruses. However, Micronbrane is actively working on upgrading NGS library kit to detect DNA/RNA viruses.
PaRTI-Seq™ can be performed on any sequencing platform including Illumina, Nanopore etc.
Yes, PaRTI-Seq™ can be both used for manual and automatic protocol. You can learn how to integrate PaRTI-Seq™ in your NGS workflow in manual here.
Generally, we recommend clinical specimens be processed as soon as practicable. The lab’s existing sample-batching policies for PCR testing should be applicable to the PaRTI-Seq™ workflow. For typical molecular workflows, possible stopping points are:
• Storage of extracted DNA in -20°C
• Holding of library prep in thermal cyclers after PCR
• Other stopping points as defined in the user’s sequencing workflow
Devin™ filter and PaRTI-Seq™ are RUO and can be validated for diagnostic use as part of a lab developed test (LDT) in a clinical setting.
Micronbrane produces and provides consumables, reagents for sample preparation, microbial DNA enrichment and NGS library construction so you only will require a sequencing platform in your lab or clinical setting for using PaRTI-Seq™ for rapid pathogen detection within 24H. Micronbrane also may provide its proprietary software for analysis of sequencing data and analytical reports (upon request). See all products here.
You can use various solutions available on the market. Please read White Paper about Clinical Bioinformatics solutions for more information.
Micronbrane is currently developing its own bioinformatic software PaRTI-Cular™ for fast analysis of sequencing data and automatic reporting on pathogens in samples. PaRTI-Cular™ contains up-to-date pathogen database (1400 known human pathogens for immediate identification) and allows to obtain full report within 30 mins (*GCP cloud). Beside that PaRTI-Cular™ includes proprietary reference database on healthy individuals for comprehensive analysis and more informed clinical picture. Unknown novel exotic pathogens with no known sequences in Micronbrane’s database may also be uncovered through bioinformatic deep analysis of unaligned sequences with the full Genbank database.
*** Currently we have limited data on viruses, yeasts, filamentous fungi, parasites and intracellular bacteria. If you have interest to participate in testing these pathogens using clinical samples, we are delighted to invite you to collaborate with us and join “Clinical Research Program” to test more sample types (You check all areas of research interest here.