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Analysis Proposal: ad_genetic_risk_loci:ABCA7 -> ABCA7 [data_in]

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analysis proposal Created: 2026-04-27T08:44:30 By: analysis_proposal_generator Quality: 50% ✓ SciDEX ID: analysis_proposal-a35ca9ac-64f0-4cd6-b8b

Analysis Proposal

Analysis Question

Can we validate ABCA7 as an Alzheimer's disease genetic risk locus by corroborating its reported GWAS associations, effect sizes, and population-specific risk contributions?

Datasets

GWAS Catalog (NHGRI-EBI)NIAGADS (NIA Genetics of Alzheimer's Disease Data Storage Site)UK Biobank Phenotype BH16.0 AD endpointsLOAD (Late-Onset Alzheimer's Disease) Consortium GWAS meta-analysis

Methods

Systematic GWAS lookup: query GWAS Catalog API for ABCA7 gene boundary variants (chr9:27500000-28500000 GRCh38) with AD/FTD phenotypesStatistical validation: extract odds ratios, 95% CI, p-values, and sample sizes for significant ABCA7 hits (p<5e-8)Cross-database corroboration: verify reported associations against NIAGADS variant-level summary statisticsEffect size heterogeneity analysis: assess population-specific effects (APOE ε4 stratified) and pleiotropy with lipid metabolism traits

Expected Outputs

List of genome-wide significant ABCA7 variants with allele frequencies, OR, and 95% CI by ancestry
Quantified confidence score for ABCA7 AD genetic risk locus status (support: high OR + replicated GWAS hits; refute: no independent GWAS signal after APOE adjustment)
Evidence item count confirming data_in relation provenance from GWAS datasets
Flagged low-confidence edge if no independent ABCA7 signals survive multiple testing correction

Related Entities

ad_genetic_risk_loci:ABCA7 ABCA7

Metadata

_origin	{'url': None, 'type': 'internal', 'tracked_at': '2026-04-27T08:44:30.140489'}
methods	['Systematic GWAS lookup: query GWAS Catalog API for ABCA7 gene boundary variants (chr9:27500000-28500000 GRCh38) with AD/FTD phenotypes', 'Statistical validation: extract odds ratios, 95% CI, p-value
datasets	['GWAS Catalog (NHGRI-EBI)', "NIAGADS (NIA Genetics of Alzheimer's Disease Data Storage Site)", 'UK Biobank Phenotype BH16.0 AD endpoints', "LOAD (Late-Onset Alzheimer's Disease) Consortium GWAS meta-
edge_count	1
source_entity	ad_genetic_risk_loci:ABCA7
target_entity	ABCA7
edge_signature	["ad_genetic_risk_loci:ABCA7\|ABCA7\|data_in"]
confidence_range	[0.0, 0.0]
expected_outputs	['List of genome-wide significant ABCA7 variants with allele frequencies, OR, and 95% CI by ancestry', 'Quantified confidence score for ABCA7 AD genetic risk locus status (support: high OR + replicate
source_relations	['data_in']
analysis_question	Can we validate ABCA7 as an Alzheimer's disease genetic risk locus by corroborating its reported GWAS associations, effect sizes, and population-specific risk contributions?

📊 Evidence Profile

Evidence Balance

+0%

Certainty

Debates

Incoming

Outgoing

0 supporting 0 contradicting 0 neutral

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Analysis Proposal: ad_genetic_risk_loci:ABCA7 -> ABCA7 [data_in]

💬 Discussion