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Next-generation Sequencing for Drug resistant TB: Webinar Series, February 5, 2019
Implementing WGS and Culture-free NGS: An Overview of Challenges and Solutions
Timothy C. Rodwell MD, PhD, MPH & the FIND NGS TeamSenior Scientific Officer (FIND)
Associate Professor of Medicine (UCSD)
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Topics to be covered
Benefits of Culture-free Sequencing for Drug Susceptibility
Testing (DST)
The Target Product Profile for NGS Diagnosis of DR-TB
NGS Workflow challenges using primary clinical samples
Bioinformatics challenges
Regulatory challenges
Implementing NGS for Diagnosis of Drug-resistant TB
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Phenotypic Drug Susceptibility Testing
Culture 6-9 WEEKS Drug Susceptibility Testing
Phenotypic Drug Susceptibility Testing
Slow Significant hands-on time
Significant biosafety hazards Requires specialized laboratories
Min potential for costs reductions Not optimal for national/global networking
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Cx-Free Next Gen Sequencing Drug Susceptibility Testing
NGS Drug Susceptibility Testing
Rapid Huge potential for automation
Minimal biosafety hazards Benchtop workflow
Rapidly decreasing costs (batching, tech,
reagents)
Designed for national/global networking
2-3 DAYS
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Minimal acceptable characteristics
Direct from sputum sample (culture-free, no BSL3)
Setting: Central TB Reference Laboratory (Level 3)
• Optimal: District hospital (Level 2)
Detect primary 1st and 2nd line drug resistance mutations (XDR+PZA)
• Open design – expandable to new mutations (e.g. Delamanid, Bedaquiline) and additional
features (surveillance, Tx monitoring)
Cost should be <60 USD (library prep + seq) per test (WGS 100 USD)
LOD: tNGS - 5,000 Mtb genomes (Scanty AFB ~103 genomes/mL); WGS - 2x105 Mtb genomes
• Optimal: 100 genomes
Heteroresistance detection: 500-R/4500-S (10%)
• Optimal: 1-R/99-S
https://www.who.int/tb/publications/2018/WHO_technical_guide_nextgen_sequencing/en/
Target Product Profile for detection of resistance associated mutations in
Mycobacterium tuberculosis complex utilizing Next Generation Sequencing
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1. Uncertainties in predicting DR phenotypes from genotypes
2. Difficulty of sequencing from direct clinical samples
3. Complexity of workflows and high costs
4. Expertise required for analysis and clinical interpretation
5. Lack of regulatory standards and guidance
Challenges to Global Implementation of NGS for DR TB Diagnosis
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Source: https://academic.oup.com/jac/article/66/7/1417/786529
Predicting XDR-TB Phenotypes with mutations in M. tuberculosis
Overcoming the Challenges
Drug resistance is acquired through spontaneous mutation
• No horizontal gene transfer
Clonal expansion
Mutations in <15 genes confer >90% of M/XDR-TB (high sensitivity)
• MICs
• Mixed populations
Expression of resistance is reliable (high specificity)
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A DNA Signal to Noise Issue
Image Source: DNA molec image: https://www.huffingtonpost.com/anne-wojcicki/science-education-fuels-i_b_3149540.html
Sequencing from Direct Clinical Samples - Challenge
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Image Source: Global Laboratory Initiative (GLI)
Sequencing from Direct Clinical Samples - Solutions
Enriching the TB DNA Signal
WGS Targeted NGS
Early MGIT Cx ( adds 1-5 days)
Multiplex PCR (1-4 hours)Differential lysis (in development)
RNA Baiting (adds sig cost & time)
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Technological Complexity of NGS - Challenge
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Instruments shown are for demonstration purposes only and not intended to indicate endorsement
Stand-Alone or Cloud-Based
Software & KnowlegebaseDNA Extraction Instrument
(automated)
Sequencer
(automated) Library Preparation
(manual)
Sputum sample
DNA extraction Library preparationTargeted
sequencingData analysis & interpretation
Standardized Result Report
Technological Complexity of NGS - Solutions
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Instruments shown are for demonstration purposes only and not intended to indicate endorsement
Cost of Goods
Targeted NGS - $50-$100 per sample
WGS - $150-$200 per sample
Cost of NGS – Challenges and Solutions
DNA Extraction Instrument
(automated)
Sequencer
(automated) Library Preparation
(manual)
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• Compute intensive
• Requires high-level expertise
• QA/QC and validation
Ezewudo et al. Sci Rep. 2018 Oct 18;8(1):15382. doi: 10.1038/s41598-018-33731-1
Bioinformatics - Challenges
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genTBPhyResSE
TB Profiler
Bioinformatics - Solutions
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Source: Tornheim et al. Clin Infect Dis – in final revision
Standardized Clinical Reporting
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Phenotypic Data
Clinical Data
SNPs
• Fully automated processing and analysis of Mtb sequences
• Integration of new genotypic, phenotypic & clinical data
• Iteratively improved interpretation and standardized reporting
for surveillance and clinical diagnosis
Bioinformatics - Solutions
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• ReSeqTB pipeline and knowledgebase being transferred to cluod
under WHO authority (ReSeqWHO - April 2019)
• Platform for global DR TB Surveillance program
• Data analysis, management and reporting
• Knowledgebase – genotypic and phenotypic data
• Eventually diagnostics (2020)
• Country agreements on data-sharing already in place
• Interoperability and data-sharing with key TB databases
• CRyPTIC, EBI (2021)
• Living knowledgebase
• Periodic review of confidence-graded mutations by
international community of TB experts (1st Review 2020)
• Inform strategy and policy for NGS (ongoing)
ReSeqWHO
Bioinformatics - Solutions
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The Regulatory Landscape
NGS-based Dx of DR-TB falls under the category of In Vitro
Diagnostics (IVD)
The first regulatory guidance for NGS IVDs was released by FDA in
2018 for Dx of Germline Diseases
EMA guidance regarding how NGS IVD solutions will be handled under
the new IVDR regulations is still evolving
Country-specific guidance on regulation of NGS IVD solutions is still
evolving
Regulatory Environment – Challenges
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FIND has been working closely with WHO and global
partners to build a foundation of knowledge and evidence
to support WHO technical guides, guidelines and
eventually policy
• Existing Guides/Reports
- Interpreting mutations conferring resistance to TB
drugs
- NGS for detecting drug-resistance conferring
mutations
• Future
- WHO endorsed list of mutations for Dx DR-TB (2020)
- Policy for use of NGS for diagnosis of DR-TB (~2021)
Regulatory Environment – Solutions for the Global Market
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FIND global market strategy for NGS as Dx for DR-TB
• Seek WHO endorsement of commercial end-to-end NGS solutions
• Submit WHO endorsed solutions to the Global Drug Facility (GDF)
catalog for listing and purchase in LMICs with Global Fund/domestic
support
Proposed path to GDF listing
• Complete analytical evaluation of existing commercial, culture-free, end-
to-end NGS solutions for Dx of DR-TB (2019)
• Conduct a clinical trial of end-to-end solutions meeting TPP criteria
(2020)
• Submit trial data to WHO for review (2021)
• Submit solutions receiving WHO endorsement to GDF catalog (~2021)
Instruments shown are for demonstration purposes only and not intended to indicate endorsement
Regulatory Environment – Solutions for the Global Market
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Where we will succeed
1. WHO DR TB surveillance will be based largely on NGS
2. 1-3 sample-to-answer targeted NGS solutions for Dx DR TB potentially endorsed by WHO
3. Cost of goods (COGs) in high-throughput labs in LMICs: $40-$50 per sample
4. Time from sample-to-answer of ~48hrs
5. There will be a global network of NGS data for DR TB
By 2022
Where we will need to continue to work on
1. Low TB DNA yield in direct clinical sample NGS
2. Genetic markers of resistance for novel and repurposed TB drugs
3. Data sharing
THE FUTURE of Cx-free NGS for Surveillance and Diagnosis of DR TB
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“Most people overestimate what they can do in one
year and underestimate what they can do in ten years.”
Bill Gates
THE FUTURE
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Swiss Development and Coop eration;State Secretariat for Education, Research andInnov ation
Neth erlands Enterprise Ag ency
Funding and Partners
FIND TB NGS Team
Anita Suresh
Rebecca Colman
Swapna Uplekar
Claudia Denkinger
Ranga Sampath
Thank you