Evolution of Next Generation Sequencing Technology: Ready for Patient Management?

Transcription

1 Evolution of Next Generation Sequencing Technology: Ready for Patient Management? Timothy Rodwell MD, PhD, MPH Senior Scientific Officer at FIND 3 rd December 2015, Union Meeting Cape Town

2 Clinical Utility of NGS for TB Diagnostics High Throughput Rapid drug susceptibility testing (RDST) for guiding therapeutics Anti-Microbial Resistance (AMR) Surveillance Culture-free surveillance for guiding regional and national rollout of new drug regimens and molecular diagnostics Treatment monitoring for Drug resistant TB Detection and monitoring of low frequency drug resistance alleles Contact Tracing and Transmission Mapping 2

3 Clinical Utility of NGS for TB Diagnostics High Throughput Rapid drug susceptibility testing (RDST) for guiding therapeutics Anti-Microbial Resistance (AMR) Surveillance Culture-free surveillance for guiding regional and national rollout of new drug regimens and molecular diagnostics Treatment monitoring for Drug resistant TB Detection and monitoring of low frequency drug resistance alleles Contact Tracing and Transmission Mapping 3

4 Whole Genome vs Targeted NGS for RDST Whole Genome Sequencing Strengths Full genome sequenced Comprehensive solution Weaknesses Slower Can t yet get Mtb WGS direct from sputum consistently More expensive More complicated bioinformatics Targeted Next Gen Sequencing Strengths Up to 200 gene targets sequenced Sequence DNA direct from sputum Faster Less expensive Weaknesses Need some knowledge of targets Not comprehensive 4

5 Steps in an NGS Pipeline DNA Extraction Amplification and Library Prep NGS Sequencing Mutation Detection Clinical Interpretation 5

6 NGS for Rapid DST of Drug Resistant TB Advantages Fast (relative to phenotypic DST) Open platform Easily and quickly adaptable to new genes and mutations Comprehensive (compared to array/probe-based platforms) High throughput Disadvantages Slower relative to array/probe-based molecular diagnostics Higher cost relative to array/probe-based molecular diagnostics High throughput 6

7 Status of NGS for Rapid DST of Clinical Samples Today US - PSQ is in use for Rapid DST of clinical samples at state and national level (AFB+ sputa and clinical TB Cx) UK Illumina WGS is in use for comprehensive clinical and epidemiological characterization of clinical strains - Proof of concept study in eight clinical labs to demonstrate that the method is feasible and costeffective Germany Research Center Borstel provides Illumina WGS analysis for RDST of MDR-TB clinical samples from TB Cx 7

8 Status of NGS for Rapid DST of Clinical Samples Near Future Global NGS solution suitable for high throughput RDST direct from sputum and deployable in reference laboratories in LMICs - Simplified - Standardized - Validated - Minimum expertise to operate 8

9 Steps in an NGS Pipeline DNA Extraction Amplification and Library Prep NGS Sequencing Mutation Detection Clinical Interpretation 9

10 Proposed Simplified, Standard Pipeline for Targeted NGS Automated DNA Extraction Simplified PCR/library Prep + Targeted NGS Variant Analysis, interpretation and archiving 10

11 Proposed Simplified, Standard Pipeline for Targeted NGS Automated DNA Extraction Completed a landscape analysis of commercially available clinical sample processing platforms Developing TPPs System Format # Identified Sample Type Technology Capacity Processing Time Manual 3 Diverse Extraction columns single 4-20mins Semi-automated 3 Diverse Magnetic bead mins Fully automated 12 Diverse Magnetic bead mins 11

12 Proposed Simplified, Standard Pipeline for Targeted NGS Simplified PCR/library Prep + Targeted NGS Multiple Groups Developing Solutions Translational Genomics Research Institute (TGen) & UCSD Rutgers University & CDC Thermo Fisher Scientific biomérieux 12

13 Targeted NGS for RDST from Sputum: A Proof of Principal Study (PI Dave Engelthaler) 13

14 Goal Goal Demonstrate that targeted NGS could be used to detect ~90% of XDR-TB phenotypes from remnant Mtb DNA extracted directly from TB patient sputa Demonstrate that (R/S) mixed populations as low as 1% could be detected in clinical samples using targeted NGS

15 Methods Design Retrospective lab study of remnant DNA extracted previously from patient sputa as part of a large prospective diagnostics trial 1 Patient Population Drug resistant TB suspects Moldova NTP NGS Targets katg Isoniazid resistance inha promoter Isoniazid resistance rpob Rifampicin resistance gyra Fluoroquinolone resistance rrs Amikacin, Kanamycin and Capreomycin resistance eis promoter Kanamycin resistance 1 Catanzaro etc al. PLoS ONE, 2015

16 Results Success of Targeted NGS unpublished data not shown

17 Heteroresistance/Mixed Populations The presence of mixtures of susceptible and resistant phenotypes in the same population May originate from superinfections of multiple strains with differing phenotypes or from evolution of original infecting strain into multiple lineages in situ Selection of resistant strains in the presence of the drug can result in treatment failure. The sooner resistance alleles are detected the more likely we can alter patient treatment to prevent treatment failure

18 SMOR: Single Molecule Over-lapping Reads Read 1 Read 2 Colman et al, PloS ONE, 2015

19 SMOR Error Calculation Standard baseline error for Illumina 1X10-2 SMOR Error = error on both reads: Product rule T A C Read 1 T A G Read 1 1x10-2 Read 2 T A G Colman et al, PloS ONE, x10-2 * 1x10-2 = 1x10-4

20 SMOR analysis

21 Clinical Heteroresistance Analysis Unpublished data not shown 10% 1% 0.1% Colman et al, PloS ONE, 2015

22 INH - Mixtures Unpublished data not shown Colman et al, PloS ONE, 2015

23 RIF - Mixtures Unpublished data not shown 2 Colman et al, PloS ONE, 2015

24 Next Steps Add new targets pnca and ahpc added Mutations for predicting phenotypic resistance to PA-184, Bedaquiline and Delamanid being developed Optimize running conditions simplify workflow

25 Proposed Simplified, Standard Pipeline for Targeted NGS Automated DNA Extraction Simplified PCR/library Prep + Targeted NGS Variant Analysis, interpretation and archiving 25

26 Proposed Simplified, Standard Pipeline for Targeted NGS Developing a solution for automated NGS bioinformatics Cloud-based TB WGS Specific No expert knowledge required for use DTBE CDC and DAIDS NIAID 26

27 Conclusions High concordance between phenotypic DST, NGS RDST results and pyrosequencing Using the SMOR methodology we were able to detect mixed populations (S/R) with high confidence direct from patient sputa which has novel clinical ramifications Targeted NGS appears to be valid means of doing culture-free RDST but will need some optimization to simplify it sufficiently for global deployment in LMICs

28 Acknowledgements FIND Claudia Denkinger David Dolinger NGS Development David Engelthaler, Rebecca Colman & NGS Team (TGen) Antonino Catanzaro, Donald Catanzaro, Valeriu Crudu (UCSD & Moldova) David Alland (Rutgers University) Jamie Posey (CDC) ReSeqTB DTBE CDC and DAIDS NIAID 28