Genomic Proficiency Test
The DTU Genomic Proficiency Test is organized and provided by the Research Group on Global Capacity Building at the Technical University of Denmark (DTU) to support global harmonization and standardization in Whole Genome Sequencing (WGS) and bioinformatics analysis. The main objective is to enable laboratories worldwide to generate comparable, high-quality genomic data for surveillance and research purposes.
What is the DTU Genomic Proficiency test (GPT)?
The GPT evaluates a laboratory’s ability to perform DNA extraction, sequencing, and WGS-based analysis of bacterial isolates. Each year, participants can receive six bacterial strains representing three different genera, provided as either lyophilized cultures or swabs.
Laboratories can sign-up for each species separately, allowing flexibility based on capacity or interest.
Participants are required to:
- Extract and purify genomic DNA
- Prepare sequencing libraries
- Sequence the isolates using short-read Illumina technology
- Analyse the data and report on:
- Multi-Locus Sequence Typing (MLST)
- Identification of acquired antimicrobial resistance (AMR) genes and AMR-associated mutations
- In silico prediction of the AMR phenotype
- Characterization of plasmids
In addition, participants must submit the raw FASTQ files for independent assessment of sequence quality, and an MD5 checksum file for verification of file integrity.
Participating laboratories are free to use any software tools or pipeline they consider appropriate for the analyses.
Why participate in the DTU GPT?
The GPT is an important tool for assessing and improving your laboratory’s capacity to perform high-quality WGS-based bacterial genomics and resistome profiling. Through the participation in the GPT, laboratories can:
- Benchmark their performance
- Identify strengths and weaknesses in their workflows
- Implement improvements in technical and analytical procedures
- Contribute to the global effort in building capacity for genomic surveillance
Technologies covered
Only paired-end short-read sequencing (e.g., Illumina) is currently included in the proficiency test.
Long-read sequencing technologies (e.g., Oxford Nanopore Technologies) are not yet supported.
Who can participate?
The following laboratories are invited to participate:
- Laboratories affiliated with the Fleming Fund project, SeqAfrica, and SeqAsia initiatives
- Laboratories that are part of the EURL-AR network
Please note: The GPT is not open to participation from external or non-invited laboratories.
Costs for participation
- No participation fee is required for laboratories affiliated with the Fleming Fund project, SeqAfrica or SeqAsia.
- Laboratories belonging to the EURL-AR network will be contacted directly to clarify the costs of participation.
Please note: All participating laboratories are expected to cover local expenses related to the handling, DNA extraction, library preparation, and sequencing of the test strains.
How to participate
A registration link for the DTU Genomic Proficiency Test will be sent to eligible laboratories around July–August each year.
Through this link, participants will be able to:
- Select the bacterial species they wish to receive
- Provide contact information and shipping details
- Submit additional information related with the laboratory's sequencing capacity
Please ensure that all contact details are accurate to avoid delays in receiving further instructions and test materials.
Please note: Any additional information and documents relevant for participants will be sent directly by email after the registration.
Import Permits
If your institution requires a permit to receive UN3373 Biological Substance, Category B from Denmark, please ensure you apply for the relevant import permit as early as possible.
Send a copy of the valid import permit to the GPT coordinator (contact below) as soon as possible, to avoid any delays.
Results and Reporting
We strive to share all materials and results with participants as soon as possible. While we do not set strict deadlines, delays may occasionally occur, and we appreciate your understanding and cooperation throughout the process.
Participants will receive feedback in different stages:
- Preliminary feedback report: After the GPT closing deadline, each laboratory will receive a preliminary report summarizing the results of their bioinformatics analysis, including expected data on the MLST, AMR gene/mutations detection, AMR phenotype prediction, and plasmid characterization.
- Comprehensive comparison guide: A follow-up guide document will be shared with all participants. It includes expected results, a comparison of all participants' outputs, and guidance to help laboratories assess their own performance in the context of the group.
- Individual performance evaluation: Finally, each laboratory will receive a confidential individual report assessing the raw sequencing data submitted (FASTQ files). This includes evaluation of general sequence quality and coverage.
Additional notes:
- An anonymized summary of overall results will be published to highlight general findings from the GPT.
- Only the GPT organizers will have access to the identities of participating laboratories.
- Due to anonymization, authorship of publications will be limited to those involved in the organization and execution of the GPT.
Contact
For questions or further information, please contact:
Joana Mourão - DTU Genomic PT Coordinator
Want to Learn More?
Find more information about past GPTs here.
About the Genomic Proficiency Test 2024
About the Genomic Proficiency Test 2023
GPT 2021 Guide for performance evaluation
GPT 2022 Guide for performance evaluation
GPT 2023 Guide for performance evaluation (The guide is on its way)