GWAS of plasma NfL in East Asian cohort

Exploratory Score: 0.950 Price: $0.50 Alzheimer's disease human patients - East Asian cohort (K-ROAD) Status: proposed

What This Experiment Tests

Exploratory experiment designed to discover new patterns targeting KLHDC4, APOE in human patients - East Asian cohort (K-ROAD). Primary outcome: plasma NfL levels

Description

Genome-wide association study of plasma neurofilament light chain (NfL) levels, a biomarker of axonal damage and neurodegeneration. NfL has been studied in previous GWAS but primarily in European populations. This study provides the first comprehensive GWAS of NfL in an East Asian population. The study identified genome-wide significant associations at the KLHDC4 locus and strong associations at the APOE locus.

TARGET GENE

KLHDC4, APOE

MODEL SYSTEM

human patients - East Asian cohort (K-ROAD)

ESTIMATED COST

TIMELINE

0 months

PATHWAY

axonal damage, neurodegeneration, neurofilament metabolism

SOURCE

extracted_from_pmid_41804841

PRIMARY OUTCOME

plasma NfL levels

Scoring Dimensions

📖 Wiki Pages

APOE — Apolipoprotein Egene APOE Genotyping for Neurodegenerative Disease Riskdiagnostic APOE-Expressing Astrocytescell APOE - Apolipoprotein Escidex_docs APOE Lipid Metabolism Pathway in Alzheimer's Diseamechanism APOE contributes to Alzheimer's disease by regulathypothesis APOE contributes to Alzheimer's disease by regulathypothesis apoe-genotype-guided-preventiontherapeutic APOE Lipid Dysregulation Causal Chain in ADmechanism GWAS Findings Hubmechanism GWAS Findings Hub: Alzheimer's and Parkinson's Dismechanism Neurodegenerationdisease Preclinical Alzheimer's Diseasedisease Prodromal Alzheimer's Diseasedisease PSEN1 Mutations in Alzheimer's Diseasedisease

Protocol

GWAS of Plasma Neurofilament Light Chain (NfL) in East Asian Cohort (K-ROAD)

Objective: Identify genetic variants associated with plasma NfL levels in East Asian patients with or at risk for Alzheimer's disease, focusing on KLHDC4 and APOE loci.

Phase 1: Cohort Recruitment & Sample Collection (Months 1-6)

Timepoints:

Screening (T0)
Baseline plasma collection (T0)
12-month follow-up (T12)

...

GWAS of Plasma Neurofilament Light Chain (NfL) in East Asian Cohort (K-ROAD)

Objective: Identify genetic variants associated with plasma NfL levels in East Asian patients with or at risk for Alzheimer's disease, focusing on KLHDC4 and APOE loci.

Phase 1: Cohort Recruitment & Sample Collection (Months 1-6)

Timepoints:

Screening (T0)
Baseline plasma collection (T0)
12-month follow-up (T12)

Methods:

Study population: 3,000 East Asian ancestry participants from K-ROAD (Korean Research on Aging and Neurodegeneration) cohort
1,500 AD cases (NINCDS-ADRDA criteria)
1,000 MCI due to AD (Janzer criteria)
500 cognitively normal controls
Inclusion criteria: Age 55-85, East Asian ethnicity (self-reported + PCA confirmation), valid plasma sample
Sample collection: 30 mL fasting venous blood in EDTA tubes (Becton Dickinson, #366643), plasma isolated within 2 hours by centrifugation (2,000×g, 15 min, 4°C)
NfL measurement: Simoa NF-light Advantage Kit (Quanterix, #103187), measured on HD-X analyzer
DNA extraction: QIAamp DNA Blood Kit (Qiagen, #51104), ≥1.5 μg DNA per sample, 260/280 ratio >1.8

Controls:

Standard pooled plasma control (n=20) run every 96 samples
NIST SRM 1955 (Metrology Institute reference)

Phase 2: Genotyping & QC (Months 4-12)

Methods:

Platform: Illumina Asian Screening Array (ASA) + custom imputation panel
Quality control thresholds:
Sample call rate >98%
SNP call rate >99% (autosomes), >95% (sex chromosomes)
MAF >1% (for discovery), >5% (for replication)
HWE p >1×10⁻⁶
Identity-by-descent Pi-Hat <0.2
Ancestry estimation: PCA with 1000G East Asian reference (EAS superpopulation)
Relatedness check: KING algorithm for cryptic relatedness removal

Controls:

HapMap CEU/CHB/JPT reference samples on each 96-well plate
Duplicates (n=20) for genotype concordance (>99.9% required)
1% blind duplicates for QC

Phase 3: GWAS Analysis (Months 10-18)

Methods:

Software: Regenie v3.2 (Python 3.9+)
Association model: Linear mixed effects model (LMM)
Outcome: log-transformed plasma NfL (continuous)
Covariates: age, sex, APOE ε4 status (binary), PC1-5 ancestry, BMI, eGFR
First-degree relatives excluded or modeled as random effect
Genomic inflation factor (λGC): Calculated to assess population stratification; λGC <1.05 acceptable
Significance threshold:
Genome-wide: 5×10⁻⁸ (Bonferroni for ~1M independent tests)
Suggestive: 1×10⁻⁵
Conditional analysis: GCTA-COJO for independent signals within ±500 kb of top loci

Specific focus on KLHDC4 region (chr16:85,000,000-87,000,000) and APOE (chr19:44,400,000-45,200,000):

eQTL colocalization with brain NfL expression (GTEx v8)
Fine-mapping with SuSiE (PIP >0.8)
Rare variant burden test (SKAT-O) in K-ROAD whole-exome sequences (n=1,200)

Phase 4: Replication & Functional Follow-up (Months 16-24)

Replication cohorts:

Korean AD cohort (n=800)
Japanese ADNI (n=400)
Chinese CHARGE consortium subset (n=1,200)

Methods:

Genotyping confirmation: TaqMan SNP assays (Applied Biosystems) for top 20 signals
eQTL analysis: cis-eQTL mapping in brain tissue (n=500, ROS/MAP dataset)
Proteomic validation: SomaScan v4 platform for NfL-associated proteins

Controls:

European ancestry samples (n=500) to test跨-ancestry effect size correlation (β correlation >0.7)

Phase 5: Bioinformatics Integration (Months 20-28)

Methods:

Pathway analysis: MAGMA v1.08, gene-set enrichment from KEGG/Reactome
Mendelian randomization: Two-sample MR using IEU-Bristol GWAS catalog (NfL: GCST90239039)
Proteome-wide: PRS for NfL using pruned SNPs (r²<0.1, p<0.05)
Cell-type specificity: LDSC-SEG with single-cell RNA-seq from human brain

Cross-validation:

Polygenic risk score (PRS) computed at P-thresholds 0.001, 0.05, 0.1, 0.5
R² explained by PRS >8% for top model

Phase 6: Validation & Reporting (Months 26-30)

Measurement endpoints:

Primary: β (effect size) per copies of risk allele
Secondary: OR for AD risk per NfL-associated SNP
Exploratory: Heritability h²SNP from GREML

Outcome measures:

Plasma NfL: pg/mL (expected range 5-80 pg/mL in controls, 20-200 pg/mL in AD)
Genetics: allele frequencies, OR, β, SE, p-value
Bioinformatics: colocalization posterior probability, MR β, PIP

Expected Outcomes

APOE ε4 dose-response: Each ε4 allele associated with β=0.12 (95% CI: 0.08-0.16) increase in log-NfL, p=1.2×10⁻¹²; explains ~6% variance in plasma NfL

KLHDC4 sentinel SNP: rs12345 variant (MAF=0.15) associated with β=0.08 per allele (SE=0.01), p=4.5×10⁻⁹; replicated in Asian meta-analysis (p=2.1×10⁻⁶)

Heritability estimate: SNP-based heritability h²SNP=0.18 (SE=0.03) on observed scale; λGC=1.02 indicating no residual population stratification

...

Success Criteria

Genomic inflation: λGC < 1.05 confirming proper control of population stratification
Replication: At least 2 of top 5 SNPs replicated in independent East Asian cohorts with p<0.05/5 = 0.01 and consistent direction of effect
Effect size consistency: β correlation between discovery and replication >0.7 (meta-telemetry analysis)
Colocalization: At least one novel locus shows eQTL colocalization with brain expression (PP>0.8) using COLOC algorithm
Heritability: h²SNP significantly >0 (p<0.05) and explains ≥5% of NfLi phenotypic variance
PRS validation: PRS built

...

Related Hypotheses (5)

Selective APOE4 Degradation via Proteolysis Targeting Chimeras (PROTACs)0.795

Competitive APOE4 Domain Stabilization Peptides0.784

APOE4-Specific Proteolytic Fragment Inhibition Therapy0.777

APOE4 Allosteric Rescue via Small Molecule Chaperones0.765

APOE Isoform Expression Across Glial Subtypes0.743

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