PROJECT HELIX-HTT | Huntington’s-Adjacent Neuro-Oncology Vaccine Program

DOCUMENT CONTROL HEADER

Program: PROJECT HELIX-HTT

Sub-Program: SCF Therapeutic Vaccine Design Platform

Module: SCF-ARGEN-HTT-NO-01 Antigen-Ranking Engine

Document Code: SCF-PLAT-VENDOR-0001

Purpose: Technology Platform Selection & Assay Infrastructure Specification

EXECUTIVE SUMMARY

The SCF Antigen-Ranking Engine requires four core discovery technologies:

1. Whole Exome Sequencing (WES) / Whole Genome Sequencing (WGS)
2. RNA Sequencing (RNA-seq)
3. HLA Typing
4. Immunopeptidomics

These technologies form the foundational data layers for:

• Neoantigen discovery
• Tumor specificity scoring
• Antigen presentation prediction
• Vaccine candidate prioritization

The recommended architecture emphasizes:

• Clinical-grade reproducibility
• Regulatory acceptability
• Scalability
• Multi-omics integration
• Future IND compatibility

PLATFORM 1

WHOLE EXOME / WHOLE GENOME SEQUENCING

Purpose

Identify:

• Somatic mutations
• Indels
• Structural variants
• Gene fusions
• Neoantigen-generating mutations

Preferred Discovery Platform

Illumina

Recommended Systems:

Advantages:

• Industry standard
• FDA familiarity
• Broad vendor ecosystem
• Excellent accuracy

Alternative Long-Read Platform

PacBio Official Website

Recommended:

• Revio System

Advantages:

• Repeat expansions
• Structural variants
• Complex genomic architecture

Particularly valuable for:

• HTT repeat biology
• Repeat instability research

Bioinformatics Pipeline

Recommended:

• BWA-MEM2
• GATK
• Mutect2
• Strelka2
• Manta

Output:

• VCF
• Mutation burden
• Clonality

PLATFORM 2

RNA SEQUENCING

Purpose

Confirm:

• Gene expression
• Tumor-specific transcription
• Neoantigen expression
• Immune microenvironment

Preferred Platform

Illumina

Systems:

• NovaSeq
• NextSeq

Preferred Depth:

Single Cell Extension

10x Genomics

Recommended:

• Chromium X

Allows:

• Tumor cell profiling
• Immune cell profiling
• Microglial profiling

Spatial Transcriptomics

10x Genomics Visium

Purpose:

• Antigen geography
• Immune infiltration mapping
• Vaccine accessibility analysis

PLATFORM 3

HLA TYPING

Purpose

Determine:

• Antigen presentation capacity
• MHC Class I
• MHC Class II

Required for:

• Neoantigen prediction
• Vaccine design

Preferred Platform

Illumina

Methods:

• TruSight HLA

Advantages:

• High-resolution typing
• Clinical adoption
• Regulatory familiarity

Alternative Platform

Omixon HLA Solutions

Advantages:

• Ultra-high-resolution HLA typing
• Neoantigen programs
• Transplant-grade accuracy

HLA Analysis Software

Recommended:

• OptiType
• HLA-HD
• arcasHLA

Outputs:

• HLA-A
• HLA-B
• HLA-C
• DR
• DQ

PLATFORM 4

IMMUNOPEPTIDOMICS

Purpose

Confirm actual peptide presentation.

This is arguably the most important validation layer.

Prediction ≠ Presentation.

Immunopeptidomics verifies:

Is the peptide truly displayed on the tumor cell surface?

Preferred Mass Spectrometry Platforms

Thermo Fisher Scientific

Recommended:

• Orbitrap Astral
• Orbitrap Eclipse
• Orbitrap Exploris

Advantages:

• Industry-leading sensitivity
• Neoantigen discovery
• MHC peptide detection

Alternative Platform

Bruker Corporation

Recommended:

• timsTOF Ultra
• timsTOF SCP

Advantages:

• Single-cell compatible workflows
• Excellent peptide sensitivity

Preferred Immunopeptidomics Service Providers

Cedars-Sinai Applied Genomics, Computation & Translational Core

Broad Institute

Moffitt Cancer Center Proteomics Core

PLATFORM 5

SCF MICROENVIRONMENT LAYER

RHENOVA Biomarker Platform

Purpose:

Measure:

• Hypoxia
• Oxidative stress
• Immune suppression
• Neuroimmune compatibility

Recommended Assays

Hypoxia

Marker

HIF-1α

CAIX

VEGF

pO₂

Oxidative Stress

Marker

8-OHdG

MDA

GSH:GSSG

ROS load

Immune Terrain

Marker

CD8

IFN-γ

CXCL9

CXCL10

PD-L1

Microglial State

Marker

IBA1

TREM2

IL-1β

TNF-α

SCF DATA INTEGRATION STACK

Cloud Infrastructure

Amazon Web Services (AWS) Health & Life Sciences

or

Google Cloud Life Sciences

Analysis Layer

Recommended:

• Python
• R
• Nextflow
• Snakemake

Vaccine Ranking Engine

Inputs:

• Genomics
• Transcriptomics
• HLA
• Immunopeptidomics
• RHENOVA

Outputs:

• Antigen Priority Score (APS)
• SCF Microenvironment Score (MES)
• CNS Safety Score
• Final Vaccine Rank

RECOMMENDED MINIMUM VIABLE DISCOVERY STACK

For PROJECT HELIX-HTT Phase I:

Genomics

• Illumina NovaSeq 6000

RNA-seq

• Illumina NovaSeq 6000

HLA

• Omixon HLA Solutions

Immunopeptidomics

• Thermo Fisher Scientific Orbitrap Astral

Single Cell

• 10x Genomics Chromium X

Cloud

• AWS Health & Life Sciences

STRATEGIC NEXT STEPS

Research Pathways

1. Build SCF Antigen-Ranking Database Schema
2. Develop SCF Vaccine Candidate Knowledge Graph
3. Build AI Neoantigen Prioritization Engine

Development Pathways

1. Generate SCF-ARGEN Data Dictionary
2. Create SCF Antigen Priority Score Calculator
3. Build IND-Facing Vaccine Discovery Workflow Package

This platform stack provides a realistic, modern discovery infrastructure that is consistent with current cancer vaccine, genomics, and immunopeptidomics programs while supporting the SCF multi-omics and microenvironment-ranking framework.