PROJECT STRANDSHIFT | DNA INJURY ATLAS: Phase 2 — DNA/RNA Injury Mapping

Document Code: SCF-AMC-STRANDSHIFT-DIA-0001

Parent Program: PROJECT STRANDSHIFT

Classification: DNA Injury, Repair Deficiency, RNA Instability, and Genome-Stress Mapping Atlas

Primary Disease Focus: HTT-associated neurodegeneration, CAG repeat instability, neuroimmune activation, viral-mimicry biology

1. OBJECTIVE

To detect, classify, and map DNA breaks, DNA repair defects, replication stress, RNA instability, and downstream neuroimmune injury signals in PROJECT STRANDSHIFT.

This atlas separates:

true DNA injury
defective DNA repair
somatic CAG expansion
RNA instability
endogenous retroelement activation
viral mimicry
confirmed exogenous viral infection

2. CORE RESEARCH QUESTIONS

Research Question	Operational Assay Strategy	Atlas Output
Are DNA breaks increased in HTT-affected tissues?	γH2AX, 53BP1 foci, comet assay, long-read WGS	DNA Break Burden Map
Are repair pathways defective or maladaptive?	DNA repair gene sequencing, repair-capacity assays, protein expression	DNA Repair Defect Matrix
Does HTT CAG expansion show somatic instability?	Long-read sequencing, small-pool PCR, repeat-primed PCR	Somatic CAG Instability Map
Is RNA processing unstable?	RNA-seq, long-read transcriptomics, splice analysis	RNA Instability Atlas
Are retroelements activated?	HERV/LINE-1 RNA profiling, methylation mapping	Retroelement Reactivation Map
Is there active viral infection?	Metagenomic sequencing, viral capture sequencing, integration-site analysis	Viral Evidence Classifier

3. SAMPLE AND TISSUE PRIORITIZATION

Tier	Biospecimen	Purpose
Tier 1	Blood, PBMCs, plasma	Accessible systemic DNA injury, immune, and viral-screening layer
Tier 2	CSF	Neurodegeneration, inflammatory, extracellular nucleic-acid markers
Tier 3	iPSC-derived neurons, astrocytes, microglia	Functional mechanistic modeling
Tier 4	Brain organoids	Developmental and tissue-like injury modeling
Tier 5	Postmortem caudate, putamen, cortex	Direct disease-tissue validation
Tier 6	Matched control tissue	Disease-specific baseline comparison

4. DNA BREAK DETECTION MODULE

Injury Class	Biomarker / Method	Interpretation
Double-strand breaks	γH2AX, 53BP1, pATM	Active DNA damage response
Single-strand breaks	comet assay, PARP1 activation	Oxidative or replication-associated DNA damage
Oxidative DNA injury	8-OHdG, FPG-comet assay	ROS-mediated genome injury
Replication stress	pRPA, ATR, CHK1	Fork stalling and repeat-instability susceptibility
Micronuclei	micronucleus assay, cGAS localization	Cytosolic DNA immune activation risk
Chromosomal instability	WGS, CNV analysis, karyotyping	Structural genome disruption

5. DNA REPAIR DEFECT MODULE

Repair Axis	Priority Genes	Assay Outputs
Mismatch repair	MSH2, MSH3, MLH1, PMS1, PMS2	Somatic repeat expansion risk
Double-strand break repair	ATM, ATR, BRCA1, BRCA2, RAD51	DSB repair competence
Base excision repair	OGG1, APEX1, XRCC1, POLB	Oxidative lesion repair
Nucleotide excision repair	XPA, XPC, ERCC1, ERCC2	Bulky lesion repair
Fanconi pathway	FAN1, FANCA, FANCD2	Repeat stability and fork protection
PARP-mediated repair	PARP1, PARP2	Single-strand break repair capacity

6. HTT SOMATIC EXPANSION MODULE

Measurement	Method	Output
Inherited CAG repeat length	Clinical-grade PCR or long-read sequencing	Baseline genotype
Somatic expansion burden	Long-read sequencing, small-pool PCR	Tissue-specific expansion index
Expansion heterogeneity	Single-cell or low-input repeat profiling	Cell-type vulnerability map
Modifier-gene correlation	Genotyping + regression modeling	DNA repair modifier network
Age-related expansion dynamics	Longitudinal sampling	Expansion trajectory model

7. RNA INSTABILITY MODULE

RNA Instability Class	Assay	Interpretation
Aberrant HTT transcript	RNA-seq, long-read RNA-seq	Transcript structure abnormality
Splicing disruption	splice-junction analysis	RNA processing defect
Repeat-associated RNA toxicity	CAG-repeat RNA profiling	Toxic RNA gain-of-function risk
Noncoding RNA disruption	miRNA, lncRNA profiling	Regulatory network instability
dsRNA accumulation	J2 antibody staining, dsRNA-seq	Viral mimicry trigger
RNA editing imbalance	ADAR editing analysis	Innate immune misclassification risk

8. VIRAL MIMICRY AND RETROELEMENT MODULE

Signal Type	Method	Classification
HERV-K / HERV-W expression	RNA-seq, targeted qPCR	Endogenous retroelement activation
LINE-1 expression	RNA-seq, ORF1p/ORF2p protein assays	Retrotransposon activation
Hypomethylation of repeats	methylation sequencing	Epigenetic derepression
IFN-stimulated genes	RNA-seq, qPCR, proteomics	Antiviral-like state
cGAS-STING activation	cGAS, STING, TBK1, IRF3 assays	Cytosolic DNA sensing
Viral genome detection	metagenomic sequencing	Candidate exogenous infection

9. DNA INJURY CLASSIFICATION SYSTEM

Class	Definition	Example
DIA-I	DNA injury without repair failure	transient γH2AX elevation
DIA-II	DNA injury with repair-pathway dysregulation	ATM or FAN1 dysfunction
DIA-III	DNA injury with repeat instability	HTT somatic expansion
DIA-IV	DNA injury with RNA instability	aberrant splicing, dsRNA accumulation
DIA-V	DNA injury with viral mimicry	IFN activation without pathogen
DIA-VI	DNA injury plus confirmed viral infection	viral genome and replication markers
DIA-VII	DNA injury with apoptotic execution	caspase activation, DNA fragmentation

10. SCF FAULT ARCHITECTURE MAP

SCF Fault Tier	Biological Event	Measured Output
Tier 1	Inherited HTT expansion	CAG repeat length
Tier 2	DNA injury burden	γH2AX, comet tail moment
Tier 3	Repair deficiency	DNA repair gene/protein defects
Tier 4	Somatic expansion	tissue-specific CAG expansion
Tier 5	RNA instability	splice, repeat RNA, dsRNA signals
Tier 6	Immune sensing	cGAS-STING, IFN-I
Tier 7	Cellular fate failure	apoptosis, senescence
Tier 8	Tissue degeneration	NfL, GFAP, neuronal loss

11. PRIMARY DATA PACKAGES

Data Package	Contents
DIA-DP1	DNA break burden dataset
DIA-DP2	DNA repair gene and pathway dataset
DIA-DP3	HTT somatic expansion dataset
DIA-DP4	RNA instability and splice dataset
DIA-DP5	retroelement and viral-mimicry dataset
DIA-DP6	exogenous virome screen dataset
DIA-DP7	integrated DNA injury score dataset

12. COMPOSITE INDICES

12.1 DNA Break Burden Score

Inputs:

γH2AX burden
53BP1 foci
comet assay tail moment
micronuclei frequency

12.2 DNA Repair Deficiency Index

Inputs:

pathogenic or functional variants
repair protein expression
repair-capacity assay output
pathway-specific failure score

12.3 Somatic Expansion Instability Index

Inputs:

tissue-specific CAG expansion burden
expansion heterogeneity
modifier-gene profile
age-adjusted expansion rate

12.4 RNA Instability Index

Inputs:

aberrant splice burden
repeat RNA burden
dsRNA signal
RNA editing imbalance

12.5 Viral Mimicry Activation Score

Inputs:

IFN-stimulated gene expression
HERV/LINE-1 expression
cGAS-STING activation
absence or presence of validated viral genome

13. DECISION TREE

Evidence Pattern	Classification
DNA breaks only	DNA injury
DNA breaks + repair defects	DNA injury with repair deficiency
DNA breaks + CAG expansion	repeat-instability injury axis
DNA breaks + dsRNA + IFN response	viral mimicry candidate
HERV/LINE-1 activation + hypomethylation	endogenous retroelement activation
viral reads only without replication markers	possible contamination or latent signal
viral genome + replication transcript/protein	active viral infection candidate
DNA fragmentation + caspase activation	apoptosis-mediated DNA injury

14. CLINICAL AND TRANSLATIONAL ENDPOINTS

Endpoint Category	Candidate Measures
Genomic	CAG length, expansion burden, repair variants
DNA Injury	γH2AX, comet assay, micronuclei
RNA	aberrant splicing, dsRNA, repeat RNA
Neuroimmune	IFN-I, IL-6, TNF-α, CXCL10
Neurodegeneration	NfL, GFAP, mutant HTT burden
Viral	HERV expression, exogenous viral genome confirmation
Cell Fate	caspase activity, TUNEL, p53 activation

15. PHASE 2 SUCCESS CRITERIA

Phase 2 is complete when the program has produced:

DNA Break Burden Map
DNA Repair Defect Matrix
HTT Somatic Expansion Map
RNA Instability Atlas
Retroelement Reactivation Map
Viral Mimicry Classifier
Exogenous Viral Evidence Classifier
Integrated DNA Injury Score
DNA Injury-to-Neuroimmune Fault Architecture
Phase 3 Multi-Omics Reconstruction Input Package

16. SCIENTIFIC BOUNDARY STATEMENT

PROJECT STRANDSHIFT does not classify injured human DNA as a virus. The atlas classifies injured DNA as a genome-stress state that may produce antiviral-like signaling, endogenous retroelement activation, RNA instability, or apoptosis. Viral classification requires independent evidence of viral genome identity, replication markers, and validated exclusion of contamination.

MASTER REGISTRY INDEX

SCF-AMC-STRANDSHIFT-DIA-0001 — DNA Injury Atlas

SCF-AMC-STRANDSHIFT-DBBS-0001 — DNA Break Burden Score

SCF-AMC-STRANDSHIFT-DRDI-0001 — DNA Repair Deficiency Index

SCF-AMC-STRANDSHIFT-SEII-0001 — Somatic Expansion Instability Index

SCF-AMC-STRANDSHIFT-RII-0001 — RNA Instability Index

SCF-AMC-STRANDSHIFT-VMAS-0001 — Viral Mimicry Activation Score

SCF-AMC-STRANDSHIFT-DIA-DP1 — DNA Break Burden Dataset

SCF-AMC-STRANDSHIFT-DIA-DP2 — DNA Repair Pathway Dataset

SCF-AMC-STRANDSHIFT-DIA-DP3 — HTT Somatic Expansion Dataset

SCF-AMC-STRANDSHIFT-DIA-DP4 — RNA Instability Dataset

SCF-AMC-STRANDSHIFT-DIA-DP5 — Retroelement/Viral-Mimicry Dataset

SCF-AMC-STRANDSHIFT-DIA-DP6 — Exogenous Virome Screen Dataset

SCF-AMC-STRANDSHIFT-0001 — PROJECT STRANDSHIFT

SCF-PATH-UT-0001 — SCF Pathophysiology Protocol

SCF-DMRD-MASTER-0001 — SCF Advanced Disease Modeling & Discovery