geno2pheno[ngs-freq]: a novel tool for drug resistance testing in - - PowerPoint PPT Presentation

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geno2pheno[ngs-freq]: a novel tool for drug resistance testing in the era of next- generation sequencing Matthias Dring Max Planck Institute for Informatics AREVIR Meeting 2018 - New Strategies - May 9, 2018 Imagine the following patient

SLIDE 1

geno2pheno[ngs-freq]: a novel tool for drug resistance testing in the era of next- generation sequencing

Matthias Döring

Max Planck Institute for Informatics AREVIR Meeting 2018

New Strategies -

May 9, 2018

SLIDE 2

Imagine the following patient

May 9, 2018 2

HIV-1 positive person Genotypic drug resistance testing Sanger sequencing

Source: med.upenn.edu

Diagnosis & Treatment

Source: myhaliburtonnow.com/20094/wilberforce-clinic-opens-tomorrow/

SLIDE 3

Resistance test comes back negative

May 9, 2018 3

Selected treatment TDF + FTC + DRV

Interpretation through HIV-GRADE

SLIDE 4

Virological failure is identified during routine monitoring in month 6 after treatment initiation

May 9, 2018 4

Maybe we should investigate the resistance status again?

500 520 540 560 580 600 620 640 660 1 10 100 1000 10000 100000 BL Month 3 Month 6

Viral load Time

Monitoring

Viral load CD4

FTC + TDF + DRV

Failure!

SLIDE 5

M184I found in the second resistance test

May 9, 2018 5

Treatment has to be adjusted! Could this have been avoided?

NRTI resistance interpretation of HIV-GRADE Drug GRADE HIVdb geno2pheno FTC R R R TDF S S R DRV S S S Resistance to selected regimen

SLIDE 6

Yes it could have – if we had used next- generation sequencing

May 9, 2018 6

Next-generation sequencing (NGS)

Source: support.illumina.com

Genotypic drug resistance testing Sanger sequencing

Source: med.upenn.edu

Genotypic drug resistance testing for NGS data

HyDRA

hydra.canada.ca

PASeq

PASeq.org

SLIDE 7

Results from geno2pheno[ngs-freq] for the corresponding NGS sample

May 9, 2018 7

Drug >= 10% >= 2% FTC S R TDF S R DRV S S

SLIDE 8

Existing web servers for NGS data

May 9, 2018 8

HyDRA

hydra.canada.ca

PASeq

PASeq.org

Noguera-Julian M, Edgil D, Harrigan PR, Sandstrom P, Godfrey C, Paredes R. Next-Generation Human Immunodeficiency Virus Sequencing for Patient Management and Drug Resistance Surveillance. J. Infect. Dis. 2017;17:19752. GATAAATCTGGTCTTATTTCC GATAATTCTGGTCTTATTTCC GATAAATCTGGTCTTATTTCC GATAAATCTGCTCTTATTCCC GATAAATCTGGTCTTATTTCC GATAAATCTGGTCTTATTTCC CATAATTCTGGTCTTATTTCC GATAAATCTGGTCTTATTTCC CATAATTCTGGTCTTATTTCC

Input: raw sequencing data Read processing pipeline: filtering, mapping, variant calling

CTAGGATAAATCTGGTCTTATTTCCTTAG

---GATAAATCTGGTCTTATTTCC----
---GATAATTCTGGTCTTATTTCC----
---GATAAATCTGCTCTTATTCCC----

CTAGGATAAATCTGGTCTTATTTCC----

TAGGATAAATCTGGTCTTATTTCCT---
-AGGATAAATCTGGTCTTATTTCCTT—
-AGGATAAATCTGGTCTTATTTCCTTA-
-AGGATAAATCTGGTCTTATTTCCTTAG

Reference sequence Rules-based resistance interpretation Limitations

Time-intensive
Rules-based

interpretation only

Support for HIV-1 only
Predetermined

processing pipeline

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geno2pheno[ngs-freq] relies on frequency files

May 9, 2018 9

Excerpt from a single-nucleotide frequency file

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How does geno2pheno[ngs-freq] work?

May 9, 2018 10

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Limitations

May 9, 2018 11

1. Cozzi-Lepri,A. et al. (2015). J. Antimicrob. Chemother.

https://doi.org/10.1093/jac/dku426

2. Johnson,J.A. and Geretti,A.M. (2010). J. Antimicrob. Chemother.

https://doi.org/10.1093/jac/dkq139

Frequency files

Co-occurrence cannot be studied
NGS data need to preprocessed

Minority resistant variants

Impact needs more thorough study [1,2]
Proviral contamination possible (APOBEC)
Worst-case prediction may be too sensitive

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Why should you use geno2pheno[ngs-freq]?

May 9, 2018 12

Rapid results

Source: thenounproject.com

Only NGS service for HCV Access to statistical model

Established methods Minority detection Integrable into existing pipelines

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Where can I find geno2pheno[ngs-freq]?

May 9, 2018 13

www.geno2pheno.org http://ngs.geno2pheno.org

Döring,M. et al. (2018) geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data. Nucleic Acids Res., 10.1093/nar/gky349. https://doi.org/10.1093/nar/gky349

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Interested in real-life applications? Join our NGS workshop later today! 15:45 – 16:45 and 16:45 – 17:45

May 9, 2018 14

Source: http://blog.strategyzer.com/posts/2014/12/02/how-to-design-great-workshops

SLIDE 15

Thanks for your attention and thanks to …

May 9, 2018 15

Thomas Lengauer

Max Planck Institute for Informatics, Saarbrücken

Nico Pfeifer

Methods in Medical Informatics, University of Tübingen

Alexander Thielen

SeqIT, Kaiserslautern

Alejandro Pironti

Broad Institute, Cambridge, MA, USA

Martin Däumer

SeqIT, Kaiserslautern Institute for Virology, University of Cologne

Elena Knops Rolf Kaiser

Institute for Virology, University of Cologne

Prabhav Kalaghatgi

Max Planck Institute for Informatics, Saarbrücken

Georg Friedrich

Max Planck Institute for Informatics, Saarbrücken

Achim Büch

Max Planck Institute for Informatics, Saarbrücken

Martin Obermeier

Medizinisches Infektionslogiezentrum Berlin (MIB), Berlin Institute for Virology, University of Cologne

Eva Heger