viral metagenomics in the clinical realm: lessons learned...
TRANSCRIPT
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www.sib.swiss
Viral metagenomics in the clinical realm:
lessons learned from a Swiss-wide ring trial
International Conference on Clinical Metagenomics (ICCMg)
Dr Aitana Lebrand | Geneva, 17 October 2019
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NGS microbes typing and characterization WG
Since Sept. 2016
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Survey shows different pipelines are
used in each clinical laboratory
Would they agree on interpretation if starting from the same sample?
Is there a need for harmonizing NGS practices
(i.e. same answer, independent of workflow used)?
Organize ring trials as quality controls (end 2017 - 2018)
Need for harmonization?
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Ring trial with two increments: ground truth known
5 from incr. 1
8 artificial in-silico generated
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Ring trial participants: 5 labs, 8 pipelines in total
Institute for Infectious Diseases
Laboratory of Virology
Institute of Medical Virology
Institute of Virology
Biology department
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Evaluation of pipeline performance
Identified viruses at the species level, per pipeline, per
sample ➔ TP, FP, FN
For the negative control, false positives were mapped at
the family level
Sensitivity, precision, F1
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Nomenclature matters
Problem: the following names
▪ human adenovirus A
▪ Adenovirus 12
▪ Mastadenovirus type 31
all refer to the same species
This is the rule, not an exception...
Solution :
▪ Define a resolution level for the trial (e.g. species)
▪ Map all possible names at that resolution, e.g./human (mast)?adenovirus (type )?(A|12|31)\b/i
→ HAdV-A
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Impact of database (incr-1)
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F1 varies strongly across pipelines (incr-1)
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Coverage helps… up to a point (incr-1)
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Same sample present twice
(sequenced by 2 centers)
In incr-2, all started with same FASTQ
=> performance is poor for sample “b”
=> sample preparation has an impact
In incr-2, sample “a” was provided by
pipeline I (red). Its results improved!
=> impact of human review for
reproducibility of results
Impact of sample prep and interpretation
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More information
Read more details in our publication
Junier et al. Viral metagenomics in the clinical realm :
Lessons learned from a Swiss-wide ring trial.
Genes, 2019, 10, 655; doi:10.3390/genes10090655
Download in-silico datasets (zenodo)
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Next step
Partner with ISO17043 certified
organizations for production-level EQAs
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Dr. Aitana Lebrand
SIB Clinical Bioinformatics
Special thanks to the EQA Team
Dr Thomas Junier (SIB & EPFL)
Dr Michael Huber (Medical Virology, Uni Zh)
And to the RT participants!