PROJECT HELIX-HTT | Huntington’s-Adjacent Neuro-Oncology Vaccine Program | SCF Multi-Omics Dataset

D-WS1-001 / D-WS2-001

SCF Multi-Omics Dataset

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

Document Control

Program Code: SCF-ARGEN-HTT-NO-01

Workflow Stage: Discovery Phase

Deliverable Type: Core Multi-Omics Dataset

Purpose: Establish the integrated data foundation for antigen discovery, antigen ranking, vaccine candidate assembly, and SCF microenvironment scoring.

1. Dataset Purpose

The SCF Multi-Omics Dataset is the foundational evidence package for identifying vaccine-relevant tumor antigens. It integrates tumor genomics, transcriptomics, HLA typing, immunopeptidomics, and SCF microenvironment biomarkers into one structured dataset.

This dataset answers five core questions:

What mutations are present in the tumor?
Which mutated or tumor-associated genes are actually expressed?
Which peptides can be presented by the patient’s HLA system?
Which peptides are confirmed on the tumor surface?
Is the tumor microenvironment suitable for vaccine-mediated immune attack?

2. Required Dataset Components

Dataset Layer	Source Material	Output File	Primary Use
Tumor Genomics	Tumor DNA	MCAT	Mutation discovery
Matched Normal Genomics	Blood, buccal, or normal tissue	Germline filter	Remove inherited variants
Tumor Transcriptomics	Tumor RNA	EXAT	Expression validation
HLA Typing	Blood or tumor-normal DNA	HCM	Antigen presentation prediction
Immunopeptidomics	Tumor lysate	PAL	Confirm presented peptides
RHENOVA / SCF Microenvironment	Tumor, plasma, CSF, PBMC	MES Input File	Immune-terrain scoring

3. Biospecimen Registry

Sample ID	Sample Type	Priority	Required?	Intended Analysis
TUM-001	Fresh tumor tissue	1	Preferred	WES/WGS, RNA-seq, immunopeptidomics
TUM-002	Frozen tumor tissue	2	Acceptable	WES/WGS, RNA-seq, immunopeptidomics
TUM-003	FFPE tumor tissue	3	Backup	WES/WGS, limited RNA-seq
NOR-001	Peripheral blood	1	Required	Matched normal DNA, HLA typing
NOR-002	Buccal swab	2	Backup	Matched normal DNA
PBMC-001	PBMC fraction	Optional	Preferred	Immune profiling
CSF-001	CSF	Optional	Exploratory	CNS biomarkers
PLA-001	Plasma	Optional	Exploratory	ctDNA, inflammatory markers
LYS-001	Tumor lysate	Preferred	Required for PAL	Immunopeptidomics

4. Data Layers and Minimum Specifications

4.1 Genomics Layer

Objective: Identify somatic mutations and tumor-specific sequence changes.

Parameter	Minimum Requirement
Assay	WES or WGS
Matched normal required	Yes
Variant classes	SNVs, indels, structural variants, fusions
Output	Mutation Catalog
File format	FASTQ, BAM/CRAM, VCF, annotated TSV

Primary Output: MCAT — Mutation Catalog

4.2 Transcriptomics Layer

Objective: Confirm that candidate antigen source genes are actively expressed.

Parameter	Minimum Requirement
Assay	Bulk RNA-seq
Optional extension	Single-cell RNA-seq, spatial transcriptomics
Output	Expression Atlas
File format	FASTQ, BAM, count matrix, TPM/FPKM table

Primary Output: EXAT — Expression Atlas

4.3 HLA Typing Layer

Objective: Determine which peptides the patient can present to immune cells.

Parameter	Minimum Requirement
HLA Class I	HLA-A, HLA-B, HLA-C
HLA Class II	HLA-DR, HLA-DQ
Output	HLA Compatibility Matrix
File format	HLA allele table

Primary Output: HCM — HLA Compatibility Matrix

4.4 Immunopeptidomics Layer

Objective: Identify naturally presented HLA-bound peptides from tumor material.

Parameter	Minimum Requirement
Assay	LC-MS/MS immunopeptidomics
Input	Tumor lysate
Output	Presented peptide inventory
File format	Peptide table, spectral evidence file

Primary Output: PAL — Presented Antigen Library

4.5 SCF Microenvironment Layer

Objective: Determine whether the tumor environment supports vaccine response.

Domain	Marker Set
Hypoxia	HIF-1α, CAIX, VEGF, pO₂
Redox stress	8-OHdG, MDA, GSH:GSSG
Immune access	CD8, IFNγ, CXCL9, CXCL10
Immune suppression	PD-L1, T-cell exhaustion markers
Microglial state	IBA1, TREM2, TNFα, IL-1β

Primary Output: MES Input File — Microenvironment Suitability Dataset

5. Integrated Dataset Schema

Field	Description
Patient/Case ID	De-identified case identifier
Sample ID	Linked biospecimen identifier
Tumor type	Neuro-oncology diagnosis
Tumor region	Anatomical or spatial location
Variant ID	Mutation identifier
Gene	Gene symbol
Variant type	SNV, indel, fusion, splice, structural variant
RNA expression	TPM / normalized expression
HLA allele	Presenting allele
Predicted peptide	Candidate antigen peptide
Binding score	HLA binding prediction
Immunopeptidomics status	Confirmed / predicted only / absent
SCF-MES score	Microenvironment suitability score
CNS risk flag	Low / moderate / high
Immune escape flag	Low / moderate / high
Antigen class	Neoantigen / TAA / SCF experimental antigen

6. Quality Control Requirements

QC Domain	Acceptance Rule
Tumor purity	Must be sufficient for variant calling
Matched normal	Required for germline subtraction
RNA integrity	Must support reliable expression calling
HLA typing	Must resolve Class I and Class II alleles
Immunopeptidomics	Spectral confidence must be documented
Microenvironment markers	Must include hypoxia, redox, and immune-access domains

7. Data Integration Logic

The dataset is integrated through the following sequence:

Tumor DNA

→ Somatic mutation discovery

→ RNA expression confirmation

→ HLA presentation prediction

→ Immunopeptidomics confirmation

→ SCF microenvironment scoring

→ CNS safety filtering

→ Antigen ranking

8. Deliverable Output Package

The completed Multi-Omics Dataset must include:

Biospecimen Registry
Mutation Catalog input files
Expression Atlas input files
HLA Compatibility Matrix input files
Presented Antigen Library input files
SCF Microenvironment biomarker table
Integrated antigen-ready master dataset
QC summary report

9. Decision Readiness

This deliverable is considered complete when the dataset can support:

Neoantigen discovery
Tumor-associated antigen filtering
HLA presentation prediction
Immunopeptidomics confirmation
SCF-MES calculation
Ranked antigen candidate generation

Status

Deliverable 1 Status: Draft Complete

Next Core Deliverable: Mutation Catalog