Clinical utility of NGS for the detection of HIV and HCV resistance

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1 18 th Annual Resistance and Antiviral Therapy Meeting v Professor Janke Schinkel Academic Medical Centre, Amsterdam, The Netherlands Thursday 18 September 2014, Royal College of Physicians, London Clinical utility of NGS for the detection of HIV and HCV resistance Janke Schinkel, MD PhD Laboratory of Clinical Virology Academic Medical Center, Amsterdam 2 1

2 NGS publications M. Quinones-Matineu, J. Clin. Viroloy Issues to address Virus diversity NGS technique and systems Technical validation Clinical validation Future perspectives 4 2

3 HIV / HCVgenetic heterogeneity enzyme HIV Reverse transcriptase HCV RdRP (NS5B) Error rate Errors introduced per RNA molecule Recombination +++ (+) daily production of virions per day HIV: within host genetic evolution Shankarappa, J Virol

4 Intrahost HCV envelope evolution over time Infection 2001 / ,02 Structured population Sequencing viral genomes 1. Direct / Conventional Sanger sequencing > consensus sequence ability to detect minor variants >= 20% 2. Clonal sequencing Genetic diversity per site Variant analysis 3. NGS (next generation sequencing, deep sequencing) Single molecule sequences with great depth Bioinformatic pipeline Diversity per nucleotide position or variant analysis 8 4

5 Available platforms longer reads more errors shorter reads less errors M. Quinones-Matineu, J. Clin. Viroloy NGS analysis pipelines raw sequence reads Quality filtering read alignment (mapping against reference sequence or de novo assembly) unmapped reads mapped reads 10 5

6 comparison clonal vs. 454 sequencing (NS3 protease HCV) K.Y. Ho, submitted 11 Clonal variants not detected by 454 K.Y. Ho, submitted 12 6

7 Variant analysis: 454 vs clonal analysis frequencies < 0.1% frequency 1.32 % frequency 0.1-1% variants 39 clonal variants K.Y. Ho, submitted 13 Reproducibility of detecting minor variants D. Knapp, PlosOne

8 Detection of minor HIV resistant variants: comparing 454 with Sanger 258 naive patients on average 1700 reads B. Simen JID robustness of MV detection by 454: variability between laboratories B. Simen et al, J Virol Methods

9 comparing 454 with Illumina for detecting integrase-resistant variants control library mixing Illumina integrase clones at different 454 concentrations median coverage per nucleotide position illumina: 2.2 Milion 454: 1349 J.Z. Li, PlosOne technical summary Illumina at comparable cost 1000 * higher coverage (> higher sensitivity) Illumina higher specificity (454 more errors) downsizing to 10% of nt input current study possible without compromising sensitivity or specificity 18 9

10 clinical validation what is the relevance of detecting MV by NGS? baseline prediction of failure (NNRTI, NRTI, PI) resistance testing at failure viral tropism 19 presence of baseline minor variants and treatment failure Pooled analysis of 10 studies on MV impact on NNRTI regimes J.Z. Li et al, JAMA

11 J.Z. Li et al, JAMA NGS & prediction of failure (1) initial regimen NNRTI + NRTI B. Simen JID

12 NGS & prediction of failure (2) initial regimen: PI + NRTI B. Simen JID NGS & prediction of failure (3) 53 patients, NNRTI based regimen 454 sequencing baseline samples 5000 reads per site Messiaen, Virology

13 NGS & prediction of failure (3) Castle Study: PI + NRTIs N = 148 Lataillade, PLosOne summary baseline NGS & prediction of failure NNRTIs: MVs detected by NGS appear to predict failure, although there is some controversy NRTIs, PIs, (integrase inhibitors): MVs detected by NGS do not predict failure 26 13

14 NGS at failure does NGS detect additional relevant MVs? very few studies PI resistance mutations (Lataillade, Plosone 2012) MV (not detected by standard genotyping) infrequent, low level resistance PI resistance after failure 2nd line PI-based regimen (Fisher, J Virol. 2012) MV observed at very low frequency, mainly as singletons, or major variants detectable by sanger sequencing RT resistance mutations (D Aquila, AIDS Res Hum Retrovir. 2011) NRTI: 1/8 L74V < 20%, K65R always > 20% NNRTI: K103N always > 20% 27 viral tropism assay (R5/X4 differentiation) PPV: percentage of R5 subjects responding to Maraviroc NGS performs as good as tropism assay, better than Sanger sequencing (Kagan, PLosone 2012, AIDS Res Hum Retroviruses. 2014) 28 14

15 What about HCV? Revolution in treatment with development of DAA (protease inhibitors, NS5A inhibitors, NS5B inhibitors) Cure rates in nearby future > 95% Need for resistance testing very limited NGS used to determine persistence of resistance in patients participating in phase 1 or phase 2 trials with PIs Persistence of resistance? Telaprevir: decline of RAVS in genotype 1a pooled analysis of registration trials Sanger sequencing data months since end of treatment 15

16 Narlaprevir resistance: clonal analysis 3,5 after year dosing J. De Bruijne, J Viral Hepat Telaprevir phase 1 trial: long term follow up by deep sequencing XV Thomas, Plos One

17 Retreatment with simeprevir SVR NR NR SVR SVR O. Lenz, Gastroentrology, 2012 Sofosbuvir FDA application HCV Nucleotide analogue S282T key mutation, very rarely observed in patients First time use of NGS data used in application to describe resistance patterns observed during clinicial trials FDA developed own analysis pipelines to compare against the pipeline used by the company 17

18 different pipelines GSI pipeline FDA pipeline FDA: L159F, V321A, (+/- 320F, C316N) emerged in 2 4% of failures GSI pipeline: missed some polymorphic sites FDA pipeline Future perspectives NGS application in clinical virology Technically Reproducible detection of MV 1 20% is possible Analysis of data time consuming, not user friendly, lack of standardization Cost effective mainly when high throughput can be realized Standardization will occur Very dynamic field: new systems, kits and pipelines will appear (2016 end of 454) Clinically Could be useful at baseline for NNRTI MV detection (RT sequencing), not useful for integrase and protease inhibitors Proof that outcome is better does not exist Can be used instead of phenotypic assay to determine virus tropism Limited data on the use of NGS at failure, probably no / little added value Mainly based on 454 NGS 18

19 acknowledgements AMC Clinical Virology group Richard Molenkamp, PhD Cynthia Ho, PhD student Xiomara Thomas, PhD student Joost van Hommerig, PhD student Gaby Steba, PhD student 19