Proposal tables
Auto-generated from tables_src/generate_tables.py. Latex sources at tables/*.tex.
Table 1. Cohort comparison
| Cohort | N | Phenotyping depth | Recontact | Aim usage |
|---|---|---|---|---|
| Aim 1 WGS training cohort* | 10,000–20,000 | Extreme phenotypes (top/bottom 10% longevity & CRF) | Yes (prospective) | Aim 1 LCI training |
| Michigan Genomics Institute (MGI) | ~90,000 | Deep EMR + multi-omic + WGS | Yes (recontact-friendly consent) | Aim 1 + 2 sub-cohort |
| MPOG (Kheterpal) | Millions across 85+ hospitals | Perioperative EMR; up to 20 prospective trials | Yes (multi-center prospective) | Aim 1 + 2 BioButton sub-cohort |
| DoDSR / USAFSAM / Cooper / VETS | Hundreds of thousands | Decades of CRF + outcomes; biobanked samples | Limited (governance-dependent) | Aim 1 LCI training |
| Oracle Health EHR (Ellison) | ~150,000,000 | EHR-derived clinical phenotypes + outcomes | No (de-identified) | Aim 1 LCI external validation |
Table 2. EMHP Phase 1 gene panel × readout layers
| Gene | Category | Methylation | Expression | Circulating |
|---|---|---|---|---|
| IL-6 | Inflammatory cytokine | Promoter CpGs | qPCR | Luminex |
| IL-1β | Inflammatory cytokine | Promoter CpGs | qPCR | Luminex |
| TNF-α | Inflammatory cytokine | Promoter CpGs | qPCR | Luminex |
| NLRP3 | Inflammasome | Promoter + intronic | RNA-seq | (intracellular) |
| ASC | Inflammasome | Promoter CpGs | RNA-seq | ASC speck assay |
| Caspase-1 | Inflammasome | Promoter CpGs | RNA-seq | Active caspase-1 assay |
| VCAM-1 | Vascular inflammation | Promoter CpGs | qPCR | ELISA / Luminex |
| ICAM-1 | Vascular inflammation | Promoter CpGs | qPCR | ELISA / Luminex |
| PGC-1α | Mitochondrial biogenesis | Promoter + body | RNA-seq | (intracellular) |
| TFAM | Mitochondrial biogenesis | Promoter CpGs | RNA-seq | (intracellular) |
| SIRT1 | Sirtuin (longevity) | Promoter CpGs | RNA-seq | (intracellular) |
| SIRT3 | Sirtuin (mitochondrial) | Promoter CpGs | RNA-seq | (intracellular) |
| SIRT6 | Sirtuin (chromatin) | Promoter CpGs | RNA-seq | (intracellular) |
| GDF-15 | Stress/metabolic marker | Promoter CpGs | RNA-seq | ELISA |
| FGF-21 | Stress/metabolic marker | Promoter CpGs | RNA-seq | ELISA |
Table 3. PI specialty matrix
| Investigator | Role | Aim 1 (LCI) | Aim 2 (EMHP) | Aim 3 (Therapies) | Cohort access |
|---|---|---|---|---|---|
| Marschall S. Runge | Architect / sr.\ collab | — | — | — | Ellison + Oracle |
| Steven L. Kunkel | PI | consult | lead | lead | — |
| Brian D. Athey | co-PI | lead (model) | ML/AI | decision framework | Oracle Health |
| Sachin Kheterpal | Senior collab | MPOG access | BioButton sub-cohort | — | MPOG (5M+) |
| Scott W. Ballinger | Collaborator | mtDNA analytics | mt-resilience clock | — | — |
| Ryan E. Mills | co-Investigator | numts + pangenome | structural variation | — | — |
| Greg Farnum | Investigator | OCI pipeline | OCI + Perturb-seq | deployment | — |
Table 4. Milestone schedule
| Year | Discovery (Aims 1–3) | Product / Regulatory | Commercial / Therapeutic |
|---|---|---|---|
| Y1 | Cohort assembly · WGS pilot · BioButton procurement | Initial patent filings | — |
| Y2 | WGS at scale · LCI v1 model · EMHP Phase 1 panel selection | — | — |
| Y3 | EMHP Phase 1 panel + BioButton sub-cohort active | Diagnostic-feasibility prototype | — |
| Y4 | EMHP Phase 2 omics · Perturb-seq screens | EMHP IVD development begins | Pre-clinical lead optimization |
| Y5 | Causal-flow analysis · target prioritization | FDA / CE-Mark dossier prep | Drug-discovery hits |
| Y6 | LCI external validation @ Oracle Health | Regulatory submission | Pre-clinical efficacy / safety |
| Y7+ | Closed-loop iteration | EMHP IVD launched | Clinical trials Phase 1–3 · personalized programs |