Epigenetic CHaracterization and Observation (ECHO) Proposers Day

Transcription

1 Epigenetic CHaracterization and Observation (ECHO) Proposers Day Eric Van Gieson, Ph.D. Program Manager Biological Technologies Office (BTO) February 23, 2018

2 ECHO Program Overview

3 Determining Exposure History from the Epigenome Capture national security and health relevant history from inherent epigenetic record Initial Altered Stressor Life Period Event Recorded in the Epigenome Build a biographical description from someone s epigenome to transform forensics and diagnostics for national security applications

4 The Epigenome as a New Forensic and Diagnostic Tool 1. Suspected Exposure 2. Epigenome Analysis 3. Exposure Identification 4. Outcome Diagnostics: No treatment necessary No Exposure Forensics: Cleared suspect Diagnostics: Patient treated, epi-response Exposure Forensics: Suspect detained, further questioning ECHO program Goal: Harness the Epigenome to determine if and when someone has been exposed to WMD precursors or agents.

5 The Epigenetic Targets for ECHO mirna Chromosomal/Chromatin Changes Chromatin Accessibility Histone Modifications DNA-base modifications RNA Modifications The Epigenome involves coordinated changes to histones, non-coding RNA and DNA in a variety of modified states, controlling gene expression

6 ECHO Program Motivation Epigenetic inheritance as explanation for non Mendelian genetics DNA methylation can affect gene expression Nucleosomes repress transcription Histone code hypothesis RNA involvement in epigenetic regulation Single base resolution for epigenetic analysis Single cell resolution for epigenetic analysis Bisulfite sequencing MSP MCIP-seq Infinium 27K&WGBS Infinium 450K&WGBS TWGBS, CAB-seq TAB-seq NOME-seq snmc-seq ChIP ChIP-chip ChIP-seq ChIA-PET Mint-chIP cchip-seq Dnase footprint Dnase-chip MNase-seq Dnase-seq FAIRE-seq SONO-seq ATAC-seq 3C 4C 5C 6C Capture Hi-C Method DNA modifications Histone modifications Chromatin Accessibility Chromosome Interactions Latest discoveries in the field have introduced new epigenetic analysis tools enabling increased read depth, providing far greater specificity and sensitivity

7 Technical Areas in ECHO Program TA1 Epigenetic Signature Identification WHAT: Specific signatures for WMD and precursor exposure WHEN: Temporal resolution of when exposure occurred TA2 Deployable Platform Development Reduced size, weight, and power footprint Field forward/austere operations ROC Performance

8 TA1 Epigenetic Signature Identification Epigenetic Datasets Build a New Epigenetics Analysis Capability Human samples / exposures (Foundation: human samples) Human Organoid Animal Molecular epigenetic dataset creation and exposurespecific epigenetic signature generation Create new bioinformatics approaches to enable: State estimates and boundary analyses Correspondence measures Topographical data analysis Generate ECHO Signature Panel (ESP) Assigning temporality and specificity to exposure types Technical Risk: Determining if the signature varies depending on dose and duration of exposure Mitigation: Supplement human profiles with organoid and animal cohorts Technical Risk: Obtaining N human samples for statistical relevance Mitigation 1: New epigenetic methods and combinations of technologies reduces cohort size requirements 100x Mitigation 2: Have established clinical research partners with sample access

9 Combinations of epigenetic methods reveal more information than a single method Initial Exposure to virus X Altered Combined WGBS* Dnase I* Mnase* *THESE ARE EXAMPLE METHODS! DARPA IS NOT ENDORSING THEM! Viral Dataset Reads Viral Dataset Reads Exposure-Specific Lassa Signature

10 Temporal Resolution of Exposure: Derived from Epigenetic Data Example: Varying Rates of Modifications Post-Exposure EXPOSURE Faster and response tor Epigenetic Response Inflammation DNA Methylation ncrna Methylation Composite Time Response Histone Modification Chromatin Access Time ECHO needs to reveal temporal resolution of initial exposure event

11 ECHO TA1 Optimal Parameter Decision Points Endothelial cells B-cells T-cells NK-cells Macrophages Best Specificity, Sensitivity and Temporal Resolution Rate of TP Rate of FP Monocytes (..) Keratinocytes Exposure Likelihood Epithelial cells C / Hi-C ATAC -SEQ ChIP -SEQ Methyl -SEQ. RNA -SEQ Note: Methods and cell types referenced are only for illustration purposes and should not be used as guidance

12 TA1 Outcome: Optimized, Automated Toolkit for Signature Development Molecular Method / Assay based on Epigenetic data Data Analysis Data Integration Exposure- Specific Signatures cfdna Blood BIOFLUIDS TARGETS microvesicles Sputum mirna ECHO teams must efficiently create signatures from an optimal combination of data analysis and molecular analysis approaches

13 ECHO Technical Area 1 Metrics and Milestones TA1: Epigenetic Signature Identification Deliverables Pressure Tests Phase I 1. Epigenetic data from molecularly analyzed samples 2. Signatures for WMD related exposures (7 total) 3. Algorithms for specific identification of exposure profiles and temporal resolution of last exposure event 6 mo Molecular epigenetic dataset release (1 virus & 1 bacteria data set per team) 12 mo - Signature release (7 total 1 virus, 1 bacteria, 5 non-biological WMD exposure signatures per team) 18 mo - Target pressure test (bacterial vs. viral differential distinction) 24 mo - Multiple target pressure test (WMD, +/- 1 year temporal resolution of last exposure) Phase II 1. Validated analytical algorithms 2. Signatures for WMD related exposures (14 total) 3. Finalized computational toolkit integrated into field forward system 36 mo Expansion of signatures, 7 additional signatures per team, algorithm and signature improvements to achieve 65% PPV 48 mo Expansion of signatures, 7 additional signatures per team, continued algorithm and signature matching improvements to achieve 85% PPV

14 Human Sample Types and Availability Teams may obtain biological samples from our partners (NMRC, WRAIR) Teams may obtain additional biological, chemical, radiological, and explosive samples on their own (see full list of specific exposures on next page and in BAA (pg 6). Sample types such as buccal, nasal, sputum or blood Cell types including, but not limited to: T-cells, B-cells, and keratinocytes Note: Teams may also propose animal models and human organ chip approaches to supplement the human samples for better time-resolution, dosing control, and creation of exposure scenarios involving highly dangerous pathogens and compounds.

15 ECHO Technical Area 1 classification of exposures Exposure Category Exposure Sub-category Minimum Required List of Exposure- Specific Agents/Compounds Biological Bacterial agents* Staphylococcus aureus (MRSA) Burkholderia pseudomallei Viral agents*: Human immunodeficiency virus (HIV) Lassa fever virus Other emerging infectious diseases Chemical Chemical agent precursors Radiological Explosives Conventional agents Toxic industrial compounds Medical isotopes Isotopes associated with weapons production Explosives precursors Explosives compounds # Proposers may select exposure-specific samples from any of the additional exposure categories. Teams are strongly encouraged to address militarily relevant compounds, precursors, or agents from each of the 10 sub-categories (17 total) * Precursors in schedules 1, 2, 3 of the OPCW CWC list: Agents listed in schedules 1,2,3, of the OPCW CWC list: # Precursors should be selected based on their importance and uniqueness to a specific agent production process, while also considering the likelihood of acquiring human samples for a given precursor exposure.

16 ECHO Technical Area 1 data management Teams will be required to share all molecular epigenetic datasets on a DARPA-specified database. This will provide other teams the opportunity to build exposure-specific signatures from samples to which they do not have access, increase the power of the bioinformatics analysis algorithms, as well as provide a means for verification and validation. BAA Page 8 Teams are required to share the molecular epigenetic datasets with IV&V partners within 30 days of completing the molecular analyses for a specific exposure. IV&V partners will measure the quality of the datasets provided by each proposer team using method-specific parameters, such as read depth, error rates, and review of molecular analysis protocols. IV&V teams will identify discrepancies, which may lead to a request for teams to re-run analyses. BAA page 10 16

17 ECHO independent verification and validation Samples from Government Partners: WRAIR NMRC Others Teams may have to repeat analyses based on QA/QC Molecular Epigenetic Datasets creation Data collection and front end QA/QC of Datasets Exposure Specific Signatures creation Data deposition and back-end QA/QC Pressure test evaluations of ESP on/off platform Samples from your team GOV/FFRDC Partners : MIT-LL Others Your Team: Creation of Signatures from validated datasets GOV/FFRDC Partners: WRAIR MIT-LL NMRC Others GOV/FFRDC Partners: WRAIR MIT-LL Others Validated datasets will be shared with all teams

18 TA2 Epigenetic Deployable Platform Development Build a Computational and Bio-Analytical System Device Integration and Refinement Minimum essential set of epigenetic methods into one device DNA Histones Chromosome Multiple analyses into single classification of exposure 1. Sample Acquisition 2. Analyte extraction process 3. Molecular analysis process 4. Analytic Result: Exposure confirmation Technical Risk: Miniaturizing analytical systems through algorithm and hardware innovations Mitigation: Technologies that combine methods and analysis enable highly parallel molecular approaches with high speed

19 ECHO methodology for optimum sensitivity and specificity Bisulfite sequencing MSP MCIP-seq Infinium 27K&WGBS Infinium 450K&WGBS TWGBS, CAB-seq TAB-seq NOME-seq snmc-seq ChIP ChIP-chip ChIP-seq ChIA-PET Mint-chIP cchip-seq Dnase footprint Dnase-chip MNase-seq Dnase-seq FAIRE-seq SONO-seq ATAC-seq 3C 4C 5C 6C Capture Hi-C Method DNA modifications Histone modifications Chromatin Accessibility Chromosome Interactions Proposers will have to choose the minimum essential set of epigenetic methods to optimize sensitivity and specificity

20 Hardware System Development Challenges 1) SOA: 12+ Individual sequencing analyses ECHO: 12+ Molecular sequencing reactions simultaneously on a single field forward device 2) SOA: Run-Time is 2 days ECHO: < 30 minutes 3) SOA: NovaSeq 6000 (Weight: 1,385 lbs; Size: L5.5ft x D3ft x W2ft; Power: 125 W) ECHO: Size: 1 ft 3 ; Weight: < 10 lbs; Power: <20w Software 1) SOA: Multiple algorithms on cloud based system ECHO: Integrate into single algorithm on miniature computing platform 2) SOA: Highly trained technician interpreting analyzed data ECHO: Translate sequenced signature into exposure type and timeframe for minimally trained user All Clear Hardware + Software 1) SOA: Analytical software does not run on purpose-built compute hardware, with heavy dependence on connectivity ECHO: A new class of hardware to accommodate faster read assembly and identification in low Quality of service (QoS) environments

21 ECHO Technical Area 2 Metrics and Milestones TA2: Deployable Platform Development Deliverables Pressure Tests Phase I 1. Sample collection and preparation system, air gap permitted 2. Onboard computational system that implements spectral matching algorithms 3. Deliver and functional testing of system module prototypes, with preliminary design review of final system 18 mo Molecular reaction development at large-scale, incorporating the presequencing preparation for the 12+ emerging epigenetics analysis methods; QoS 100% 24 mo Assembly and separate functional testing of small-scale system modules: 1) nucleic acid extraction module, 2) pre-sequencing preparation, 3) sequencing; QoS 100% with intermittent coverage Phase II 1. Sample-answer device with zero air-gaps and onboard computational capability 2. Size (1 ft 3 ), weight (< 10 lbs), and power(< 20 W) footprint equivalent to today s POC diagnostics systems 3. Sample to answer time < 30 min 30 mo Transition of all molecular analysis steps to the small scale system, airgapped demonstration of epigenetic tests across all system modules; QoS 50% with intermittent coverage 36 mo Epigenetic test of all modules with <50,000 cells, 65% PPV; QoS 25% with intermittent coverage 48 mo System Demonstration, <50,000 cells, under 30 min, 85% PPV, QoS 10% with intermittent coverage with minimally-trained operators

22 ECHO Milestones and Metrics

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